US20160312312A1 - Paper-based synthetic gene networks - Google Patents

Paper-based synthetic gene networks Download PDF

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US20160312312A1
US20160312312A1 US15/102,213 US201415102213A US2016312312A1 US 20160312312 A1 US20160312312 A1 US 20160312312A1 US 201415102213 A US201415102213 A US 201415102213A US 2016312312 A1 US2016312312 A1 US 2016312312A1
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shelf
cell
paper
stable composition
reaction
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Keith PARDEE
James J. Collins
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Harvard College
Boston University
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Harvard College
Boston University
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Assigned to TRUSTEES OF BOSTON UNIVERSITY reassignment TRUSTEES OF BOSTON UNIVERSITY ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: HOWARD HUGHES MEDICAL INSTITUTE
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

Definitions

  • the present disclosure relates generally to shelf-stable compositions and methods for sensing and performing logic functions based on synthetic gene networks.
  • the field of synthetic biology aims to re-engineer the components of natural systems to solve global challenges like lowering the cost of drug production or green energy and chemistry.
  • synthetic biologists are creating whole-cell biosensors, synthetic probiotics, and new sources of drugs, green energy and novel chemistries.
  • synthetic gene networks (Lu et al., Nat. Biotechnol. 2009, 27, 1139-1150) that control the cellular factories responsible for manufacturing.
  • Hosting these engineered pathways in living cells has meant, primarily, that synthetic biology has been confined to the lab and large commercial operations.
  • aspects of the invention relate to the discovery that a lyophilized synthetic gene network and/or a cell-free system comprising components sufficient for a template-directed synthetic reaction, can retain its bioactivity when stored under room temperature for a period of time.
  • One aspect of the invention relates to a shelf-stable composition comprising a cell-free system that comprises components for a template-directed synthetic reaction, wherein the cell-free system is lyophilized on a solid support. The cell-free system can become active for the template-directed synthetic reaction upon re-hydration.
  • the shelf-stable composition further comprises a synthetic gene network.
  • the synthetic gene network comprises one or more nucleic acids.
  • the nucleic acid can comprise for example DNA, RNA, an artificial nucleic acid analog, or a combination thereof.
  • the template-directed synthetic reaction is a transcription reaction
  • the components sufficient for the transcription reaction comprise promoter-containing DNA, RNA polymerase, ribonucleotides, and a buffer system.
  • the template-directed synthetic reaction is a translation reaction
  • the components sufficient for the translation reaction comprise ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system.
  • the components can also comprise amino acids or amino acids and aminoacyl tRNA synthetases.
  • the template-directed synthetic reaction is a coupled transcription and translation reaction
  • the components sufficient for the coupled transcription and translation reaction comprise promoter-containing DNA, RNA polymerase, ribonucleotides, ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system.
  • the components can also comprise amino acids or amino acids and aminoacyl tRNA synthetases.
  • the solid support is a porous substrate, and the shelf-stable composition is partially or completely embedded in the porous substrate.
  • the porous substrate comprises paper.
  • the porous substrate comprises quartz microfiber, mixed esters of cellulose, porous aluminum oxide, or a patterned surface.
  • the solid support is pre-treated with bovine serum albumin, polyethylene glycol, Tween-20, Triton-X, milk powder, casein, fish gelatin, or a combination of one or more thereof.
  • the cell-free system comprises a whole cell extract or a recombinant protein transcription/translation system.
  • the whole cell extract is selected from the group consisting of rabbit reticulocyte lysate, wheat germ extract, E. coli extract, and human cell extract.
  • the recombinant protein transcription/translation system permits protein synthesis using recombinant elements (PURE) or PURExpress® (New England Biolabs, Ipswich, Mass.) (see Shimizu and Ueda, “Pure Technology,” Cell-Free Protein Production: Methods and Protocols, Methods in Molecular Biology, Endo et al. (Eds), Humana 2010; and Shimizu et al., “Cell-free translation reconstituted with purified components,” Nature Biotechnology 2001, 19, 751-755).
  • PURE recombinant elements
  • PURExpress® New England Biolabs, Ipswich, Mass.
  • the synthetic gene network functions as a sensor.
  • the senor can detect an analyte in an aqueous sample.
  • the detection of the analyte can produce an optical signal or an electronic signal.
  • the synthetic gene network comprises a logic circuit.
  • the logic circuit comprises an AND gate, a NOT gate, an OR gate, a NOR gate, a NAND gate, a XOR gate, a XAND gate, or a combination thereof.
  • the logic circuit is activated upon contacting with water and optionally a composition comprising a trigger.
  • the trigger is selected from the group consisting of a chemical element, a small molecule, a peptide, a protein, a nucleic acid, an extract, and a combination thereof.
  • the shelf-stable composition is shelf stable for at least two weeks.
  • a related aspect of the invention regards a shelf-stable composition
  • a shelf-stable composition comprising a cell-free system comprising components sufficient for a template-directed synthetic reaction, a synthetic gene network, and a solid support, wherein said shelf-stable composition is substantially free of water, and wherein said cell-free system is active for said template-directed synthetic reaction upon rehydration.
  • Yet another aspect of the invention regards a shelf-stable composition produced by a process, the process comprising contacting a solid support with an aqueous solution comprising a cell-free system and a synthetic gene network, and lyophilizing said solid support.
  • Another aspect of the invention regards a method of detecting an analyte, comprising providing a shelf-stable composition described herein, wherein the composition comprises a nucleic acid-based sensor, contacting the composition with the analyte in the presence of water under conditions permitting transcription and/or translation, and detecting a signal, wherein detection of the signal indicates the presence of the analyte.
  • the method further comprises a step of contacting the composition with a barrier to water evaporation or enclosing the composition in an enclosure after the contacting step.
  • the method can provide a measure of the amount of the analyte.
  • the nucleic acid-based sensor comprises a reporter gene.
  • the reporter gene encodes a fluorescence protein, an enzyme, or an antigen.
  • the nucleic acid-based sensor comprises a catalytic nucleic acid.
  • the method further comprises providing a fluorophore, whereby said fluorophore can couple to a nucleic acid to produce a change in fluorescence.
  • the analyte is selected from the group consisting of a nucleic acid, a pathogen, a pathogen extract, a metabolite, an antibiotic drug, an explosive chemical, a toxic chemical, and an industrial chemical.
  • the toxic chemical is a heavy metal or insecticide residue.
  • the signal is luminescence.
  • the signal is fluorescence
  • the signal is a visible color.
  • the signal is electronic.
  • the analyte is in an aqueous solution.
  • Another aspect of the invention regards a method of activating a synthetic gene network lyophilized on a solid support, comprising providing a shelf-stable composition described herein, wherein the composition comprises the synthetic gene network, and contacting the composition with water.
  • a related aspect of the invention regards a method of activating a lyophilized synthetic gene network, comprising providing a lyophilized cell-free system comprising components sufficient for a template-directed synthetic reaction, and contacting the lyophilized synthetic gene network with the lyophilized cell-free system in the presence of water.
  • Yet another aspect of the invention relates to a kit comprising the shelf-stable composition described herein and packaging materials thereof.
  • the kit further comprises an enclosure, wherein said enclosure encloses the composition during a template-directed synthetic reaction to slow or prevent water evaporation.
  • compositions, methods, and respective component(s) thereof are used in reference to compositions, methods, and respective component(s) thereof, that are useful to an embodiment, yet open to the inclusion of unspecified elements, whether useful or not.
  • shelf-stable refers to the bioactivity (e.g., gene expression level, enzyme activity, or biosynthetic activity upon re-hydration) of the compositions described herein changing no more than 30% upon storage at room temperature (i.e., about 20° C. to 24° C.) and relative humidity of no more than 10% for two weeks. Stated another way, if the bioactivity of the shelf-stable composition re-hydrated on the day it's lyophilized (referred to as the first-day bioactivity herein) is set as 100%, then after two-week storage, the bioactivity of the composition is no less than 70%.
  • a shelf-stable composition can also mean a composition that can regain at least 3% of the first-day bioactivity after storage for about 3 months, preferably at least 5%, at least 10%, at least 12%, at least 15%, at least 18%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or more of the first-day bioactivity.
  • the shelf-stable composition is stored in an environment with relative humidity of 60%.
  • the shelf-stable composition is stored in an environment with relative humidity of less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, less than 1%, or less than 0.1%.
  • the shelf-stable composition is stored in a humidity-controlled environment (e.g., a desiccator or a containing comprising a desiccant).
  • the shelf-stable composition is stored in a an environment comprising nitrogen gas greater than 79% by volume, greater than 85% by volume, greater than 90% by volume, or greater than 95% by volume.
  • the shelf-stable composition is stored in a container that blocks natural light.
  • the percentage of light being blocked can be more than 5%, more than 10%, more than 15%, more than 20%, more than 25%, more than 30%, more than 35%, more than 40%, more than 45%, more than 50%, more than 55%, more than 60%, more than 65%, more than 70%, more than 75%, more than 80%, more than 85%, or more than 90%.
  • the term “substantially free of water” means that the water content in a composition is no more than 5% by weight.
  • the term encompasses, for example, a water content of no more than 4%, no more than 3%, no more than 2%, no more than 1%, no more than 0.5%, or no more than 0.1% by weight.
  • cell-free system refers to a set of reagents capable of providing for or supporting a biosynthetic reaction (e.g., transcription reaction, translation reaction, or both) in vitro in the absence of cells.
  • a cell-free system comprises promoter-containing DNA, RNA polymerase, ribonucleotides, and a buffer system.
  • Cell-free systems can be prepared using enzymes, coenzymes, and other subcellular components either isolated or purified from eukaryotic or prokaryotic cells, including recombinant cells, or prepared as extracts or fractions of such cells.
  • a cell-free system can be derived from a variety of sources, including, but not limited to, eukaryotic and prokaryotic cells, such as bacteria including, but not limited to, E. coli , thermophilic bacteria and the like, wheat germ, rabbit reticulocytes, mouse L cells, Ehrlich's ascitic cancer cells, HeLa cells, CHO cells and budding yeast and the like.
  • eukaryotic and prokaryotic cells such as bacteria including, but not limited to, E. coli , thermophilic bacteria and the like, wheat germ, rabbit reticulocytes, mouse L cells, Ehrlich's ascitic cancer cells, HeLa cells, CHO cells and budding yeast and the like.
  • biosynthetic reaction is used herein to refer to any reaction that results in the synthesis of one or more biological compounds (e.g., DNA, RNA, proteins, monosaccharides, polysaccharides, etc.).
  • a transcription reaction is a biosynthetic reaction because RNA is produced.
  • Other examples of biosynthetic reactions include, but are not limited to, translation reactions, coupled transcription and translation reactions, DNA synthesis, and polymerase chain reactions.
  • in vitro refers to activities that take place outside an organism. In some embodiments, “in vitro” refers to activities that occur in the absence of cells. As used herein, a reaction occurring on a porous solid substrate in the absence of viable cells is an in vitro reaction.
  • porous substrate refers to a substrate that contain pores or interstices via which a liquid composition may penetrate the substrate surface. Paper is one example of a porous substrate.
  • synthetic biological circuit is used herein to refer to any engineered biological circuit where the biological components are designed to perform logical functions. In general, an input is needed to activate a synthetic biological circuit, which subsequently produces an output as a function of the input.
  • a synthetic biological circuit comprises at least one nucleic acid material or construct.
  • a synthetic biological circuit is substantially free of nucleic acids.
  • a synthetic gene network is one kind of synthetic biological circuit.
  • Other examples of synthetic biological circuits include, but are not limited to, an engineered signaling pathway, such as a pathway that amplifies input via kinase activity.
  • “Synthetic gene network” or “synthetic gene circuit” are used interchangeably herein to refer to an engineered composition that comprises at least one nucleic acid material or construct and can perform a function including, but not limited to, sensing, a logic function, and a regulatory function.
  • the nucleic acid material or construct can be naturally occurring or synthetic.
  • the nucleic acid material or construct can comprise DNA, RNA, or an artificial nucleic acid analog thereof.
  • the nucleic acid materials or constructs can interact with each other directly or indirectly. An indirect interaction means that other molecules are required for or intermediate in the interaction.
  • Some examples of synthetic gene networks comprise a nucleic acid operably linked to a promoter.
  • operably linked indicates that a promoter is in a correct functional location and/or orientation in relation to a nucleic acid sequence it regulates to control transcriptional initiation and/or expression of that sequence.
  • nucleic acid As used herein, the terms “nucleic acid,” “polynucleotide,” and “oligonucleotide” are used interchangeably to generally refer to any polyribonucleotide or poly-deoxyribonucleotide, and includes unmodified RNA, unmodified DNA, modified RNA, and modified DNA.
  • Polynucleotides include, without limitation, single- and double-stranded DNA and RNA polynucleotides.
  • nucleic acid embraces chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the naturally occurring chemical forms of DNA and RNA found in or characteristic of viruses and cells, including for example, simple (prokaryotic) and complex (eukaryotic) cells.
  • a nucleic acid polynucleotide or oligonucleotide as described herein retains the ability to hybridize to its cognate complimentary strand.
  • An oligonucleotide is not necessarily physically derived from any existing or natural sequence, but can be generated in any manner, including chemical synthesis, DNA replication, DNA amplification, in vitro transcription, reverse transcription or any combination thereof.
  • a “promoter” refers to a control region of a nucleic acid sequence at which initiation and rate of transcription of the remainder of a nucleic acid sequence are controlled.
  • a promoter can also contain sub-regions at which regulatory proteins and molecules can bind, such as RNA polymerase and other transcription factors. Promoters can be constitutive, inducible, activatable, repressible, tissue-specific or any combination thereof.
  • a promoter drives expression or drives transcription of the nucleic acid sequence that it regulates.
  • signaling pathway refers, unless context dictates otherwise, to the components of a signaling pathway.
  • signaling pathway lyophilized on a solid support refers to components necessary for the signaling pathway of interest, lyophilized on the solid support.
  • reference to a “gene network” lyophilized on a solid support is a reference to the components of such a network lyophilized on the support.
  • template-directed synthetic reaction is used herein to refer to a synthetic reaction for which a nucleic acid template guides the pattern of nucleic acid or amino acid addition to a nucleic acid or polypeptide polymer.
  • DNA replication and transcription are template-directed synthetic reactions that produce DNA or RNA products, respectively using a DNA template. Reverse transcription produces a DNA product using an RNA template.
  • Translation is a template-directed synthetic reaction that produces a polypeptide or protein using an RNA template.
  • active or “activated” are used interchangeably herein to refer to the readiness of a shelf-stable composition described herein or a portion thereof to perform an innate function or task.
  • Reaction components lyophilized on a solid support are “activated” by addition of water or an aqueous sample, regaining transcription and/or translation activities.
  • the composition or a portion thereof performs the function or task when it's active or activated.
  • the composition or a portion thereof does not perform the function or task when it's active or activated, but is ready to do so when an external factor (an analyte or trigger as non-limiting examples) is provided.
  • a lyophilized reaction/component mixture that regains at least 3% of its original activity upon re-hydration is considered “active.”
  • the mixture regains at least 10%, at least 12%, at least 15%, at least 18%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or more of its original activity (i.e., activity just prior to lyophilization).
  • the regained activity is comparable to the original activity when the difference between the two is no more than 20%.
  • sample means any sample comprising or being tested for the presence of one or more analytes.
  • samples include, without limitation, those derived from or containing cells, organisms (bacteria, viruses), lysed cells or organisms, cellular extracts, nuclear extracts, components of cells or organisms, extracellular fluid, media in which cells or organisms are cultured in vitro, blood, plasma, serum, gastrointestinal secretions, ascites, homogenates of tissues or tumors, synovial fluid, feces, saliva, sputum, cyst fluid, amniotic fluid, cerebrospinal fluid, peritoneal fluid, lung lavage fluid, semen, lymphatic fluid, tears, pleural fluid, nipple aspirates, breast milk, external secretions of the skin, respiratory, intestinal, and genitourinary tracts, and prostatic fluid.
  • a sample can be a viral or bacterial sample, a sample obtained from an environmental source, such as a body of polluted water, an air sample, or a soil sample, as well as a food industry sample.
  • a sample can be a biological sample which refers to the fact that it is derived or obtained from a living organism. The organism can be in vivo (e.g. a whole organism) or can be in vitro (e.g., cells or organs grown in culture).
  • a sample can be a biological product.
  • a “biological sample” also refers to a cell or population of cells or a quantity of tissue or fluid from a subject.
  • a “biological sample” will contain cells from a subject, but the term can also refer to non-cellular biological material, such as non-cellular fractions of blood, saliva, or urine, that can be used to measure analyte or enzyme activity levels, for example, upon rehydration.
  • Biological samples also include explants and primary and/or transformed cell cultures derived from patient tissues.
  • a biological sample can be provided by removing a sample of cells from subject, but can also be accomplished by using previously isolated cells or cellular extracts (e.g., isolated by another person, at another time, and/or for another purpose).
  • Archival tissues such as those having treatment or outcome history can also be used.
  • Biological samples include, but are not limited to, tissue biopsies, scrapes (e.g.
  • sample also includes tissue biopsies, cell culture.
  • sample also includes untreated or pretreated (or pre-processed) samples. For example, a sample can be pretreated to increase analyte concentration.
  • the term “trigger” refers to a composition, molecule, or compound that can activate a synthetic gene network.
  • analyte is used herein to refer to a substance or chemical constituent in a sample (e.g., a biological or industrial fluid) that can be analyzed (e.g., detected and quantified) and monitored using the sensors described herein.
  • a sample e.g., a biological or industrial fluid
  • an analyte include, but are not limited to, a small inorganic or organic molecule, an ion, a nucleic acid (e.g., DNA, RNA), a polypeptide, a peptide, a monosaccharide, a polysaccharide, a metabolic product, a hormone, an antigen, an antibody, a biological cell, a virus, and a liposome.
  • small molecule refers to a natural or synthetic molecule having a molecular mass of less than about 5 kD, organic or inorganic compounds having a molecular mass of less than about 5 kD, less than about 2 kD, or less than about 1 kD.
  • portable refers to a device that can be held by a person of ordinary strength in one or two hands, without the need for any special carriers.
  • a portable device can be configured to be used outside of a laboratory setting.
  • a portable device is, e.g., battery powered.
  • FIGS. 1A-1B show that freeze-dried cell-free systems can retain bioactivity and can be stored over a period of time.
  • FIG. 1A shows time course experiments of constitutive GFP expression from DNA template using fresh and freeze-dried transcription and translation reactions. Freeze-dried reactions had expression activity comparable to fresh reactions.
  • FIG. 1B shows that extracts stored at room temperature with desiccant pack and a nitrogen-rich environment appear to maintain stable transcription and translation activity (at least 120 days). GFP expression from DNA template using a T7 RNA polymerase based system.
  • FIGS. 2A-2B show that freeze-dried whole bacterial cell extracts support inducible expression from an E. coli RNA polyermase (RNAP) based construct.
  • RNAP E. coli RNA polyermase
  • FIG. 2A GFP ( FIG. 2A ) and mCherry ( FIG. 2B ) expression was induced from the TetO promoter using a chemical analog to the antibiotic doxycycline (e.g., anhydrotetracycline, aTc).
  • aTc antibiotic doxycycline
  • FIGS. 3A-3C show that freeze-dried T7 cell-free expression systems ( FIG. 3C ) have comparable expression characteristics to T7-mediated expression in E. coli ( FIG. 3A ) or T7-based fresh reaction ( FIG. 3B ).
  • Freeze dried T7 whole extracts or recombinant cell-free systems can support inducible expression from plasmid DNA, linear dsDNA and ssRNA templates.
  • GFP expression is induced from Toe-hold switches (riboswitches) by short trigger RNA.
  • FIG. 4 shows that hydrophobic rings can be used to create reaction regions on a paper substrate. Hydrophobic ink was applied to paper, briefly heated to remove water and ensure ink fully spanned the thickness of the paper. Using a humid chamber, various expression constructs were tested at load volumes of 0.5, 1.5 and 3 uL.
  • FIGS. 5A-5C show that embedded freeze-dried cell-free expression systems support transcription and translation reactions on quartz microfiber or filter paper discs (both pre-treated with 50 mg/ml BSA).
  • FIG. 5A shows inducible expression of GFP or mCherry from pTetO-based DNA template using 11 uM aTc. Reactions were embedded into quartz microfiber.
  • FIG. 5B shows inducible expression of fluorescent reporter proteins from Toe-hold switches using freeze-dried T7-based expression system embedded into paper discs. In the presence of the correct RNA trigger, expression is induced.
  • FIG. 5C shows that using a freeze dried cell-free expression system embedded into paper, GFP expression is repressed from Toe-hold repressor in the presence of the correct RNA trigger.
  • FIG. 6 is a graphic representation of how 4 fluorescent reporters could be deposited onto a larger sheet of paper, using hydrophobic barriers printed using a wax-based laser printer or other method of printing or lithography to separate the reactions spaces. Protein expression from four toe-hold switches (56, 69, 96, 117) could be alternately activated or not using trigger RNA.
  • FIGS. 7A-7H are time course data of GFP expression from eight Toe-hold switches: 56 ( FIG. 7A ), 69 ( FIG. 7B ), 96 ( FIG. 7C ), 117 ( FIG. 7D ), PA ( FIG. 7E ), PB ( FIG. 7F ), PC ( FIG. 7G ), PD ( FIG. 7H ) using freeze dried T7-based cell-free reactions (7 ul volume, no paper).
  • Time course data show that translation-only reactions (from RNA; solid lines) are induced more quickly than transcription-translation reactions (from DNA; dotted lines). The time savings comes from pre-transcribing the RNA riboswitch, so that in the presence of trigger RNA translation occurs immediately. RNA copies of the riboswitch are less stable than DNA copies in the freeze-dried systems.
  • FIGS. 8A-8B show a comparison of TetO-based induction between standard cell extracts and cell extracts doped with tetR before freeze drying. By adding tetR prior to freeze-drying, leaky expression for the tetO promoter is minimized, resulting in much greater fold-change and control over gene expression.
  • FIG. 9 is a colorimetric reporter system based on the expression of the enzyme chitinase.
  • the fluorescent reporter protein gene from tetO_GFP has been removed and replaced with chitinase.
  • expression of chitinase is activated.
  • the enzyme cleaves the colorless 4-Nitrophenyl N,N′-diacetyl-beta-D-chitobioside substrate to yield a yellow p-nitrophenol product.
  • FIGS. 10A-10C show toe-hold switch mechanism and sensors based on toe-hold switches.
  • FIG. 10A is a schematic of the toe-hold switch mechanism. Activation of the toe-hold switch by the trigger RNA leads to expression of the reporter gene, which can be for example, a fluorescent reporter protein, an enzyme or other functional protein.
  • the reporter gene can be for example, a fluorescent reporter protein, an enzyme or other functional protein.
  • the enzyme LacZ is expressed and cleaves the yellow chlorophenol Red- ⁇ -D-galactopyranoside (CPRG) substrate to produce the purple chlorophenol red product.
  • FIG. 10B shows development of color on paper discs using this LacZ-based colorimetric output can be seen developing beginning around 25 min.
  • FIG. 10C are images of colorimetric data from Toe-hold switches 56, 69 and 96 with and without RNA trigger induction. From a freeze-dried preparation on 2 mm paper discs.
  • FIGS. 11A-11B show that paper- or quartz-based reactions perform better when paper or quartz has been pre-treated.
  • FIG. 11A shows that paper-based reactions perform better when paper has been pre-treated, washed and then dried before reactions are added (without wishing to be bound by theory, it is thought that pre-treatment reduces adsorption of reactions components to cellulose fibers).
  • Paper was tested for best treatment agent with BSA (column 2), PEG (column 3), Triton X-100 (column 1), skim milk, and tween-20 (column 4). Column 5 is the control. In the end, the best performer was determined to be 5% BSA.
  • quartz-based reactions perform better when quartz has been pre-treated, washed and then dried before reactions are added (without wishing to be bound by theory, it is thought that pre-treatment reduces adsorption of reactions components to quartz fibers).
  • the quartz microfiber was tested for best treatment agent with BSA (column 1), PEG (column 2), Triton X-100 (column 3), skim milk, and tween-20 (column 4). Column 5 is the control.
  • FIGS. 12A-12B show demonstrations of mRNA sensors.
  • FIG. 12A In the presence of super-folder GFP (sfGFP) mRNA, the GFP mRNA sensor is activated and expresses mCherry (GFP is also expressed from target GFP mRNA).
  • FIG. 12B In the presence of mCherry mRNA, the mCherry mRNA sensor is activated and expresses GFP (mCherry is also expressed from target mCherry mRNA). This was used as a proof of concept for sensing active full-length mRNA.
  • FIGS. 13A-13B show that mRNA sensors can be used for antibiotic resistance genes.
  • FIG. 13A Freeze dried reactions supported the detection of mRNA resistance genes in solution, using a plate reader to measure GFP output.
  • FIG. 13B Freeze dried reaction supported the detection of mRNA resistance genes on paper discs, using the LacZ enzyme-mediated colorimetric output.
  • FIGS. 14A-14D show how microfluidics could be used to deliver sample to more than one sensor in a device, as well as to control evaporation.
  • FIG. 14A is a graphic representation showing two sensors connected by a microfluidic channel.
  • FIG. 14B is a demonstration of how plastic films can be used to create microfluidics for the delivery of sample to more than one disc.
  • FIG. 14C is a graphic representation showing a cross section of a design for FIG. 14A .
  • FIG. 14D is a graphic representation showing four sensors connected by microfluidic channels.
  • FIG. 15 shows chitin beads hydrated with a cell-free system containing DNA template for a Toe-hold RNA sensor and the complementary RNA trigger.
  • FIG. 16A is a schematic of paper-based synthetic gene networks. Enzymes necessary for transcription, translation, or both are combined with engineered gene circuits, and then embedded and freeze dried into paper to create stable and portable synthetic gene networks outside of the cell context. These networks can include, for example, genetically encoded tools with trigger, regulatory transducer and output elements.
  • FIG. 16B is a plot showing GFP expression in solution phase from fresh and freeze-dried PT7 cell-free reactions.
  • FIG. 16C is a plot showing that freeze dried pellets of the PT7 cell-free expression system are stable for months, yielding GFP expression when rehydrated.
  • FIG. 16D is a schematic of the constitutive GFP expression constructs used on paper.
  • FIG. 16E is a set of images and fold change measurement of constitutive paper-based GFP expression from freeze-dried S30, S30 T7 and PT7 cell-free systems during the first 90 minutes of incubation.
  • FIG. 16F is a schematic of the TetO regulation of GFP or mCherry.
  • FIG. 16G is a set of images and fold change measurement of GFP and mCherry from the TetO promoter, +/ ⁇ aTc inducer, from freeze-dried S30 reactions. aTc concentration used 11 uM.
  • FIGS. 17A-17C demonstrate freeze-dried, RNA-actuated, gene circuits on paper.
  • FIG. 17A is a set of images of paper-based GFP expression from eight toehold switches (A-H) in the PT7 cell-free system, +/ ⁇ complementary trigger RNAs.
  • FIG. 17B is a set of plots showing maximum fold change measurement of GFP expression from toehold switches A-H during the first 90 minutes of incubation.
  • FIG. 17C is a set of images showing RNA-actuated expression of GFP, venus, mCherry and cerulean fluorescent proteins from toehold switch H on paper and quartz microfiber discs.
  • FIG. 17D is a set of bright field and fluorescence images of an orthogonality screen between toehold switches and trigger RNAs using paper-based reactions arrayed in a 384 well plate.
  • FIG. 17E is a plot showing quantification of fluorescence over time from paper discs containing switch G (bottom row). All data were generated from freeze-dried, cell-free reagents embedded into paper with their respective gene circuits. Trigger RNA concentration used for toehold switch activation, 5 uM.
  • FIGS. 18A-18I demonstrate colorimetric output from paper-based synthetic gene networks.
  • FIG. 18A is a schematic of modified, LacZ expressing toehold switches used to generate colorimetric outputs.
  • FIG. 18B is a set of images of paper-based, colorimetric output from toehold switches A-H, +/ ⁇ complementary RNA triggers.
  • FIG. 18C is a set of plots showing maximum fold change measurements from LacZ toehold switches A-H during the first 90 minutes of incubation. Fold induction based on the rate of color change from LacZ toehold switches.
  • FIG. 18D is a set of images showing the paper-based development of color from LacZ toehold switch D over 60 minutes.
  • FIG. 18E is a plot where color intensities from FIG. 18D converted to blue and yellow (red+green) channels and graphed over time.
  • FIG. 18F is a schematic describing the process of arraying synthetic gene networks on paper using printed arrays.
  • FIG. 18G is an image of a 25-reaction printed array, with positive and control reactions distributed in a checkerboard pattern.
  • FIG. 18H is a schematic of a low cost, electronic optical reader developed to read colorimetric output from paper-based synthetic gene networks. Paper-based reactions are held in a chip between an LED light source (570 nm) and electronic sensor.
  • FIG. 18I is a plot of time course date from the electronic optical reader of toehold switch G in the presence of 0, 30, 300 and 3000 nM trigger RNA. All data were generated from freeze-dried, cell-free reagents embedded into paper with their respective gene circuits.
  • FIG. 19A is a schematic of the paper-based mRNA sensors based on toehold switches.
  • FIG. 19B presents images and fold-change measurements of a paper-based mCherry mRNA sensor in the presence and absence of full-length target mRNA. GFP is produced in response to detection of mCherry mRNA.
  • FIG. 19C presents Images and fold-change measurements of a paper-based GFP mRNA sensor in the presence and absence of full-length target mRNA. mCherry is produced in response to detection of GFP mRNA.
  • FIG. 19D is a plot showing fold change of the LacZ-mediated color output rate from sensors for mRNAs encoding resistance to spectinomycin, chloramphenicol, ampicillin and kanamycin antibiotics.
  • FIG. 19E is a plot showing fold change of the color output rate from the ampicillin resistance sensor using the purpose-built electronic optical reader over a titration of mRNA concentrations.
  • FIG. 19F presents images and fold-change measurement of constitutive paper-based GFP expression from a freeze-dried Hela cell extract.
  • FIG. 19G is a schematic of the FRET-based mechanism used in the glucose nanosensor.
  • FIG. 19H is a plot showing that 528 nm fluorescence is reduced in response to glucose binding to the FRET-based glucose nanosensor expressed on paper. All data were generated from freeze-dried, cell-free reactions embedded into paper with their respective gene circuits.
  • FIGS. 20A-20B are plots showing solution phase reactions from freeze dried pellets.
  • FIG. 20A GFP expression from S30 cell extracts.
  • FIG. 20B GFP expression from S30 T7 cell extracts.
  • FIGS. 21A-21F show TetO regulated paper-based expression of mCherry and GFP over time.
  • FIGS. 21A-21B are plots showing time course expression of TetO-regulated mCherry and GFP.
  • FIGS. 21E-21F are plots showing fold change of fluorescence output from aTC induce TetO mCherry and GFP, relative to uninduced controls. RFU, relative fluorescence units. Error bars represent standard deviation.
  • FIGS. 22A-22B show tetR supplementation of S30 extracts for TetO regulation improves fold change measurements. Error bars represent standard deviation. RFU, relative fluorescence.
  • FIG. 22A is a plot showing aTc induction of TetO GFP in the absence and presence of tetR supplementation prior to freeze drying.
  • FIG. 22B is a plot aTc induction of TetO mCherry in the absence and presence of tetR supplementation prior to freeze drying. Error bars represent standard deviation.
  • FIG. 23 is a set of plots showing paper-based regulation of GFP expression from toehold switches A-H.
  • the red dots indicate the time point from which maximum fold change calculations reported in FIG. 17B were taken.
  • FIG. 24 is a set of plots showing rate of paper-based GFP expression from toehold switches A-H.
  • the red dots indicate the time point from which fold change calculations reported in FIG. 17B were taken.
  • RNA trigger concentration 5 um. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 25 is a set of plots showing fold change of fluorescence output from RNA induced toehold switches, relative to uninduced controls. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 26 is a plot showing titration of RNA trigger for toehold switch D in solution phase reactions. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 27 is a set of plots showing comparison of toehold switch induction in E. coli and from freeze-dried, paper-based reactions.
  • FIGS. 28A-28B show paper-based regulation of four fluorescence reporter proteins from toehold switch H.
  • FIG. 28A a set of plots showing paper-based regulation of GFP, venus, mCherry and cerulean fluorescent proteins by toehold switch H over a time course.
  • FIG. 28B is a set of images of quartz microfiber discs each embedded with three toehold switches (switch H_GFP, switch A_cerulean and switch C_mCherry). The four discs carrying these switches were rehydrated and incubated with either water or trigger RNAs for H, A or C. The individual activation of these switches was imaged using the green, blue and red fluorescence channels. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIGS. 29A-29C are experimental data showing fold change and time course data for the color outputs from toehold switch H.
  • FIG. 29A is a set of plots showing Maximum fold change measurement of venus, mCherry and cerulean expression from toehold switches H during the first 90 minutes of incubation.
  • the red dots indicate the time point from which fold change calculations reported in FIG. 29A were taken.
  • FIG. 29C is a set of plots showing fold change of fluorescence output from RNA induced toehold switch H, relative to uninduced controls. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 30 is a set of plots showing paper-based regulation of LacZ colorimetric response from toehold switches A-H over time. Colorimetric response was quantified as a measure of absorbance at 570 nm. The red dots indicate the time point from which fold change calculations reported in FIG. 18C were taken. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 31 is a set of plots showing rate of color change from LacZ toehold switches A-H over time. Colorimetric response was quantified as a measure of absorbance at 570 nm. The red dots indicate the time point from which fold change calculations reported in FIG. 18C were taken. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 32A is a set of plots showing rate-based fold change for LacZ colorimetric response paper-based from toehold switches, relative to uninduced controls. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 32B is a composite image of orthogonality screen of LacZ colorimetric toehold switch reactions on paper discs arrayed in a 384-well plate.
  • FIGS. 33A-33D show an alternative chitinase-based colorimetric output on paper.
  • FIG. 33A is a plot showing maximum fold change of the colorimetric TetO_chitinase output at 420 mins.
  • FIG. 33B is a set of bright field and 410 nm absorbance images of the TetO_chitinase system embedded into paper, +/ ⁇ aTc induction. Chitinase expression leads to the cleavage of a colorless precursor to generate a yellow product, which was quantified by monitoring absorbance at 410 nm.
  • FIG. 33C is a plot of time course evolution of the paper-based colorimetric reaction as measure by 410 nm absorbance.
  • FIG. 33E is a plot of fold change of absorbance output from aTc-induced TetO chitinase relative to uninduced control. Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIGS. 34A-34D are experimental data showing titration of full-length target mRNA for paper-based antibiotic resistance gene mRNA sensors with LacZ output. Summary of rate-based fold change for LacZ mRNA sensors for ( FIG. 34A ) kanamycin, ( FIG. 34B ) spectinomycin, ( FIG. 34C ) chloramphenicol and ( FIG. 34D ) ampicillin resistance gene (Plate reader, Abs 570 nM). Values presented are the average of either triplicate or quadruplicate data. Error bars represent standard deviation.
  • FIG. 35A is a plot of time course for the ampicillin resistance sensor from the low cost, electronic optical reader. Values presented are the average of either triplicate or quadruplicate data.
  • FIG. 35B is a plot showing measurement of fold change of LacZ rate by paper-based ampicillin resistance gene mRNA sensor with LacZ output over time.
  • FIG. 36 is a plot of fluorescence spectrum of FRET-based glucose nanosensor in the presence and absence of 10 mM glucose. Using freeze-dried, cell-free expression in Hela cell extracts, the 528 nm fluorescence peak of the nanosensor is suppressed in the presence of glucose as previously reported. RFU, relative fluorescence units.
  • FIGS. 37A-37D is a set of images showing that blocking paper and quartz microfiber improves the efficiency of GFP expression.
  • FIG. 37A Toehold switch H_GFP reactions on 2 mm paper discs that have been blocked with 5% BSA, 5% Triton X-100, 5% PEG 8k, 5% Tween-20 or washed with water.
  • FIG. 37B Toehold switch B_GFP on paper discs treated as above
  • FIG. 37C Toehold switch H_GFP on 2 mm quartz microfiber discs treated as above
  • FIG. 37D Toehold switch B_GFP on quartz microfiber discs treated as above.
  • FIGS. 38A-38B show components used in the fabrication of an optical electronic reader.
  • FIG. 38A 570 nm LED light source and luminosity sensors are coordinated to the chicken Micro through two multiplexers.
  • FIG. 38B Line drawings used to cut the reader housing from black acrylic using a laser printer.
  • FIGS. 39A-39E demonstrate rapid prototyping of paper-based RNA sensors for sequences from Sudan and Zaire strains of the Ebola virus.
  • FIG. 39A is a schematic of the generation of Ebola RNA sensors. Sensors with the same letter were targeted to identical windows in the Ebola nucleoprotein mRNAs of their respective strains.
  • FIG. 39B is a plot showing twenty-four toehold switch-based RNA sensors were constructed and tested in a 12 h period. Based on the RNA segment windows (A-L), maximum fold change during the first 90 minutes at 37° C. is reported for both the Sudan and Zaire strains of the virus. Fold change rate is determined from the slope of absorbance at 570 nm over time ( ⁇ control, +3000 nM RNA trigger).
  • FIG. 39C is a composite image of the 240 paper-based reactions used to test the 24 sensors. Control and untriggered toehold sensors remain yellow and activated toehold sensors have turned purple.
  • FIG. 39D is a plot showing sequence specificity tested for four Sudan and four Zaire sensors from the original set of 24. Each of the four sensors targeting Sudan sequences were treated with 3000 nM of OFF-target RNA sequence from the complementing Zaire RNA sequence, and vice versa.
  • FIG. 39E is a set of plots showing fold change of the color output rate of sensors SD and ZH over a titration of RNA concentrations.
  • FIGS. 40A-40D demonstrate paper-based converging transcriptional cascade.
  • FIG. 40A is a schematic of the genetically encoded components that convert transcription from E. coli RNAP into transcription from T3 RNAP and/or T7 RNAP. Expression of these new RNAPs drive the transcription of previously dormant GFP constructs with T3 or T7 promoters, as well as a toehold switch and trigger pair under the regulation of T7 and T3, respectively.
  • FIG. 40B present images and fold-change measurements of paper-based T3 GFP expression with and without T3 cascade module.
  • FIG. 40C present images and fold-change measurements of paper-based T7 GFP expression with and without T7 cascade module.
  • FIG. 40D present images and fold-change measurements of paper-based T3/T7-dependent GFP expression with and without T3 and T7 cascade modules. All data were generated from freeze-dried, cell-free reactions embedded into paper with their respective GFP expression constructs; cascade modules were added as DNA components at rehydration. Data were collected after an overnight incubation.
  • a lyophilized synthetic gene network and/or a cell-free system comprising components sufficient for a template-directed synthetic reaction, can retain its bioactivity when stored under room temperature for a period of time.
  • the synthetic gene network and/or the cell free system can become activated, and can perform in the same or similar manner compared to a counterpart that is hosted in a living cellular system.
  • green fluorescent protein GFP
  • FIG. 1A green fluorescent protein (GFP) can be produced after a freeze-dried cell-free system is activated; and the GFP can emit green fluorescence, indicating that the protein is properly folded and active.
  • the described devices and methods were developed to exploit this discovery, and can be broadly applicable in areas including, but are not limited to, point-of-care diagnostics, clinical and industrial settings, and consumer goods.
  • one aspect of the technology described regards a method of stabilizing a synthetic gene network and/or a cell-free system comprising components sufficient for a template-directed synthetic reaction, the method comprising lyophilizing the synthetic gene network and/or the cell-free system.
  • the lyophilization step is done onto a solid support.
  • the synthetic gene network or cell-free system regains bioactivity upon rehydration.
  • bioactivity is biosynthetic activity.
  • a related aspect of the technology disclosed herein regards a shelf-stable composition
  • a shelf-stable composition comprising a cell-free system that comprises components for a template-directed synthetic reaction, wherein the cell-free system is lyophilized on a solid support.
  • the cell-free system can become active for the template-directed synthetic reaction upon re-hydration.
  • a template-directed synthetic reaction is a transcription reaction
  • the components sufficient for the transcription reaction comprise promoter-containing DNA, RNA polymerase, ribonucleotides, and a buffer system.
  • RNA polymerases include, but are not limited to, T3 RNA polymerase, T7 RNA polymerase, and SP6 RNA polymerase.
  • a template-directed synthetic reaction is a translation reaction
  • the components sufficient for the translation reaction comprise ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system.
  • Components of translation factors are disclosed in Shimizu and Ueda, “Pure Technology,” Cell-Free Protein Production: Methods and Protocols, Methods in Molecular Biology, Endo et al. (Eds), Humana 2010; and Shimizu et al., “Cell-free translation reconstituted with purified components,” Nature Biotechnology 2001, 19, 751-755. For example, in E.
  • the translation factors responsible for protein biosynthesis are three initiation factors (IF1, IF2, and IF3), three elongation factors (EF-G, EF-Tu, and EF-Ts), and three release factors (RF1, RF2, and RF3), as well as RRF for termination.
  • initiation factors IF1, IF2, and IF3
  • EF-G elongation factors
  • RF1, RF2, and RF3 release factors
  • Exemplary cell-free systems for synthesis of proteins are disclosed in U.S. Pat. No. 6,780,607, U.S. Pat. No. 8,445,232, US20090317862, US20130053267, WO2013067523, WO2014122231, the contents of each of which are incorporated by reference in their entirety.
  • a template-directed synthetic reaction is a coupled transcription and translation reaction
  • the components sufficient for the coupled transcription and translation reaction comprise promoter-containing DNA, RNA polymerase, ribonucleotides, ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system.
  • a template-directed synthetic reaction is DNA synthesis
  • the components sufficient for the DNA synthesis comprise DNA polymerase, deoxyribonucleotides, and a buffer system.
  • the DNA polymerase can be, but need not necessarily be, a thermostable DNA polymerase.
  • a template-directed synthetic reaction is a polymerase chain reaction (PCR), and the components sufficient for PCR comprise a DNA template, primers, thermostable polymerase, deoxynucleoside triphosphates, and a buffer system.
  • PCR polymerase chain reaction
  • the cell-free system comprises a whole cell extract.
  • the whole cell extract can be an extract from any cell type from any organism.
  • the whole cell extract can be rabbit reticulocyte lysate, rabbit oocyte lysate, wheat germ extract, E. coli extract, a mammalian cell extract (e.g., human cell extract).
  • Eukaryotic extracts or lysates may be preferred when the resulting protein is glycosylated, phosphorylated or otherwise modified because many such modifications are only possible in eukaryotic systems.
  • Commercial whole cell extracts are widely available through vendors such as Thermo Scientific, Life Technologies, New England Biolabs Inc., Sigma Aldrich, and Promega.
  • Membranous extracts such as the canine pancreatic extracts containing microsomal membranes, are also available which are useful for translating secretory proteins.
  • Mixtures of purified translation factors have also been used successfully to translate mRNA into protein as well as combinations of lysates or lysates supplemented with purified translation factors such as initiation factor-1 (IF-1), IF-2, IF-3 ( ⁇ or ⁇ ), elongation factor T (EF-Tu), or termination factors.
  • IF-1 initiation factor-1
  • IF-2 IF-2
  • IF-3 ⁇ or ⁇
  • EF-Tu elongation factor T
  • the cell-free system comprises a recombinant protein transcription/translation system.
  • the recombinant protein transcription/translation system permits protein synthesis using recombinant elements (PURE) or PURExpress® (New England Biolabs, Ipswich, Mass.) cell-free transcription/translation system.
  • PURExpress® is a cell-free transcription/translation system reconstituted from the purified components necessary for E. coli translation.
  • the cell-free system can initiate a template-directed synthetic reaction simply upon rehydration (e.g., FIG. 1A ).
  • the cell-free system becomes activated for a template-directed synthetic reaction upon rehydration, but an input is needed to initiate the reaction.
  • the cell-free system is embedded partially or completely in the solid support. In one embodiment, the cell-free system is on a surface of the solid support.
  • the solid support can be in any form including, but is not limited to, a well, a tube, a planar substrate (e.g., a chip or a plate), a sphere, a porous substrate (e.g., a mesh or a foam), a 3D scaffold, a patterned surface (e.g., nano-patterns, or micro-patterns, or both), a porous or solid bead, a hydrogel, a channel (e.g., a microfluidic channel), a smooth surface, and a rough surface.
  • the solid support is hydrophilic and preferably porous.
  • a patterned surface can be physically or chemically patterned, or both.
  • a physically patterned surface is textured, and can comprise nano-patterns, micro-patterns, or both.
  • a chemically patterned surface typically comprises hydrophilic molecules and/or hydrophobic molecules attached to the surface in a desired pattern.
  • a hydrophobic surface can be patterned with hydrophilic molecules to render certain regions hydrophilic.
  • the solid support comprises a matrix capable of high capillary action.
  • High capillary action enables even distribution of a small volume of liquid over a large surface area without the use of a pump.
  • the matrix capable of high capillary action is porous and hydrophilic.
  • the solid support comprises paper.
  • Papers applicable in the technology described herein can include, but not limited to, printing paper, wrapping paper, writing paper, drawing paper, specialty paper (for example, chromatography paper, filter paper, e.g., WhatmanTM filter paper), handmade paper, or blotting paper.
  • specialty paper for example, chromatography paper, filter paper, e.g., WhatmanTM filter paper
  • white paper can act as a surface for displaying optical signals (e.g., fluorescence, luminescence, or visible color).
  • the paper is hydrophilic and preferably porous.
  • the paper is hydrophobic.
  • hydrophobic paper can become hydrophilic after treatment by a laser (Chitnis et al., Lab Chip 2011, 11, 1161), therefore one can create hydrophilic regions on hydrophobic paper by selective laser scanning.
  • the solid support comprises quartz microfiber, mixed esters of cellulose, cellulose acetate, silk, porous aluminum oxide (e.g., anopore membrane), or regenerated membrane.
  • the shelf-stable composition is lyophilized in a tube/micro-chamber and then transferred to a high capillary material upon re-hydration.
  • the solid support comprises a sticky component, thereby allowing the shelf-stable composition to stay on surfaces.
  • the solid support comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, or more spatially distinct reaction regions where the cell-free system is confined.
  • the area that contains the cell-free system is herein referred to as “a reaction region.”
  • reaction regions can be created by a chemical process such as using hydrophobic barriers on a piece of paper ( FIG. 4 or 18F ).
  • the hydrophobic barriers are minimally permeable by water.
  • the hydrophobic barrier can comprise hydrophobic materials such as hydrophobic polymer or wax.
  • the hydrophobic barrier can be patterned by any existing patterning method (e.g., micro-contact printing, or dip pen lithography, photolithography, e-beam lithography, laser printing, inject printing, or a micro-arrayer).
  • patterning method e.g., micro-contact printing, or dip pen lithography, photolithography, e-beam lithography, laser printing, inject printing, or a micro-arrayer.
  • the reaction regions can be arranged in a random or pre-determined pattern (e.g., linear, periodic, or pseudo-periodic).
  • the reaction regions can be patterned on the solid support using a patterning device (e.g., a laser printer, an inject printer or a micro-arrayer).
  • the reaction regions can also be created by a physical process such as producing wells on the solid support.
  • the solid support can be pre-treated with a protein source (e.g., bovine serum albumin, milk powder, casein, or fish gelatin), polyethylene glycol, a surfactant (e.g., polysorbate 20 or Triton-X), or a combination thereof.
  • a protein source e.g., bovine serum albumin, milk powder, casein, or fish gelatin
  • polyethylene glycol e.g., polyethylene glycol
  • a surfactant e.g., polysorbate 20 or Triton-X
  • this pre-treatment step can increase the signal-over-noise ratio for a fluorescent signal by limiting non-specific binding and/or irreversible binding of the reaction components. For example, see FIG. 37 .
  • the solid support comprises one or more fluidic channels (e.g., microfluidic channels) that connect reaction regions with an area for adding an aqueous sample.
  • fluidic channels e.g., microfluidic channels
  • the fluid is wicked away to the reaction regions, thereby a plurality of reaction regions can be activated by the same sample (for example, see FIGS. 14A-14D ).
  • the solid support can further comprise electrodes, thus allowing the solid support to interface with electronic devices.
  • electrodes can be patterned using methods including, but not limited to, photolithography, e-beam lithography, and masked evaporation.
  • methods of patterning electrodes on paper can be found in WO2009121041.
  • the solid support is a reaction chip.
  • the reaction chip can comprise a sample hosting layer, a light blocking layer, a hydration layer, a transparent layer, a humidity maintaining layer, and a water vapor permeable layer.
  • the hydration layer can comprise a hydrated material or chamber that provides humidity during incubation and/or measurement.
  • the humidity maintaining layer can be water impermeable.
  • the water vapor permeable layer can regulate humidity for the sample.
  • the shelf-stable composition further comprises a synthetic gene network.
  • Synthetic gene networks have been largely confined to research laboratories due to its reliance on living cellular systems and a lack of means for long-term storage. The inventors' discovery overcame these challenges and provided a straightforward yet highly effective solution for storing and transporting devices based on synthetic gene networks.
  • the shelf-stable composition described herein can be used in on-demand applications, which had not been achievable in the past.
  • any synthetic gene network can be applicable in the technology disclosed herein, including, but not limited to a sensor, a switch, a counter, a timer, a converter, a toggle, a logic gate (e.g., AND, NOT, OR, NOR, NAND, XOR, XAND, XNOR, A IMPLY B, A NIMPLY B, B IMPLY A, B NIMPLY A, or a combination thereof), or a memory device (e.g., volatile or non-volatile).
  • a logic gate e.g., AND, NOT, OR, NOR, NAND, XOR, XAND, XNOR, A IMPLY B, A NIMPLY B, B IMPLY A, B NIMPLY A, or a combination thereof
  • a memory device e.g., volatile or non-volatile
  • WO2014093852 describes 16 logic gates based on synthetic gene networks: AND, OR, NOT A, NOT B, NOR, NAND, XOR, XNOR, A IMPLY B, B IMPLY A, A NIMPLY B, B NIMPLY A, A, B, FALSE and TRUE.
  • Methods of constructing synthetic gene networks are also disclosed, for example, in Synthetic Gene Networks, Weber and Fussenegger (Eds.) 2012, Humana Press, the contents of which are incorporated by reference in their entirety.
  • the synthetic gene network is also lyophilized on the solid support, and resides in the same reaction region as the cell-free system. Similar to the cell-free system, the synthetic gene network becomes active upon rehydration.
  • an input e.g., an analyte, a trigger, or a combination
  • the synthetic gene network which processes the information and relays it to the cell-free system.
  • the cell-free system performs a template-directed synthetic reaction based on the information, and then generates downstream information in the form of an output (e.g., an optical signal, an electronic signal, or a combination) to the environment.
  • an output e.g., an optical signal, an electronic signal, or a combination
  • the synthetic gene network comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more nucleic acids.
  • the nucleic acid comprises DNA, RNA, an artificial nucleic acid analog, or a combination thereof.
  • the synthetic gene network functions as a sensor.
  • the sensor can detect an analyte. When the analyte contacts the shelf-stable composition in the presence of water, the analyte activates the sensor, which produces a signal, indicating the detection of the analyte.
  • the signal is optical.
  • an optical signal can be fluorescence, luminescence, absorption or reflection of a given wavelength, ultraviolet, visible color, or infrared.
  • the signal is electronic (e.g., conductivity change or capacitance change).
  • the senor comprises a reporter component.
  • the function of the reporter component is to produce a detectable signal when an analyte is detected.
  • a reporter component can be used to quantify the concentration, strength, or activity of the input received by the compositions of the invention.
  • the reporter component comprises a reporter gene.
  • a reporter gene encoding any fluorescent protein can be applicable in the invention.
  • the fluorescent protein includes, but is not limited to, for example, GFP, mCherry, Venus, and Cerulean. Examples of genes encoding fluorescent proteins that can be used in accordance with the compositions and methods described herein include, without limitation, those proteins provided in U.S. Patent Application No. 2012/0003630 (see Table 59), incorporated herein by reference.
  • a reporter gene encoding any enzyme can be applicable as well.
  • Enzymes that produce colored substrates (“colorimetric enzymes”) can also be used for visualization and/or quantification. Enzymatic products can be quantified using spectrophotometers or other instruments that can take absorbance measurements including plate readers (for example, see FIG. 26 ). Examples of genes encoding colorimetric enzymes that can be used in accordance with the compositions and methods described herein include, without limitation, lacZ alpha fragment, lacZ (encoding beta-galactosidase, full-length), and xylE.
  • An enzyme e.g., glucose oxidase
  • a nuclease enzyme can cleave a nucleic acid sequence such that an electronic and optical signal is generated.
  • an enzyme can separate a fluorescence resonance energy transfer (FRET) or quenching pair to induce a change in fluorescence.
  • FRET fluorescence resonance energy transfer
  • a reporter gene encoding any antigen for which a specific antibody is available or can be made can also be applicable.
  • antigens are expressed by the reporter gene, the antigens bind to an electrode coated with complementary antibodies, which produces an electronic signal.
  • a reporter gene can encode an antibody, which when expressed, binds to an electrode coated with the complementary antigen.
  • reporter genes see Reporter Genes: A Practical Guide, D. Anson (Ed.), 2007, Humana Press, the contents of which are incorporated by reference for examples on reporter genes.
  • a reporter gene encoding luciferases can also be used in the technology described herein. Luciferases produce luminescence, which can be readily quantified using a plate reader or luminescence counter. Examples of genes encoding luciferases for that can be used in accordance with the compositions and methods described herein include, without limitation, dmMyD88-linker-Rluc, dmMyD88-linker-Rluc-linker-PEST191, and firefly luciferase (from Photinus pyralis).
  • the reporter component comprises a catalytic nucleic acid including, but not limited to, a ribozyme, an RNA-cleaving deoxyribozyme, a group I ribozyme, RNase P, a Hepatitis delta ribozyme, and DNA-zymes.
  • a catalytic nucleic acid including, but not limited to, a ribozyme, an RNA-cleaving deoxyribozyme, a group I ribozyme, RNase P, a Hepatitis delta ribozyme, and DNA-zymes.
  • the reporter component comprises a fluorophore, a metabolite, or protein, wherein the fluorophore, metabolite, or protein can couple to a nucleic acid to produce a change in fluorescence.
  • RNA-fluorophore complexes have been reported and can be used in the compositions and methods described herein (see, e.g., Paige et al., Science 2011, 333, 642-646). RNA binding to metabolites or proteins can also lead to a change in fluorescence (see, e.g., Strack et al., Nature Protocols 2014, in press).
  • the nucleic acid can be the analyte. In another embodiment, the nucleic acid can be transcribed due to the detection of an analyte.
  • the senor or network comprises a gene that encodes a therapeutic peptide or protein, antibiotics or other therapeutic agent that is produced in response to a specific set of conditions, e.g., pathogen presence.
  • the sensor(s) or network (s) can be embedded into wound dressing/bandaids for infection monitoring and alert with colorimetric output and/or produce therapeutic agents.
  • the senor is an RNA sensor.
  • the RNA sensor can detect a full-length RNA or a fragment thereof.
  • the RNA sensor can detect messenger RNA (mRNA).
  • an RNA sensor was created based on the principles of toe-hold switches ( FIG. 10A ).
  • the rational programmability of toehold switches comes from their design.
  • Riboregulators are composed of two cognate RNAs: a transducer RNA that encodes the output signal of the system (e.g. a GFP mRNA) and a trigger RNA that modulates the output signal.
  • Conventional riboregulators have historically repressed translation by sequestering the ribosomal binding site (RBS) of the transducer RNA within a hairpin. This hairpin is unwound upon binding of a cognate trigger RNA, exposing the RBS and enabling translation of the downstream protein.
  • RBS ribosomal binding site
  • RNA sensors based on toehold switches can be found, for example, in WO2014074648, the contents of which are incorporated by reference in their entirety.
  • the reporter component comprises the gene that encodes the enzyme LacZ.
  • the analyte being detected is a specific RNA molecule, which can activate the translation of LacZ in the presence of a cell-free system comprising components for the translation.
  • LacZ is known in the art to cleave the yellow chlorophenol Red- ⁇ -D-galactopyranoside (CPRG) substrate to produce the purple chlorophenol red product.
  • CPRG yellow chlorophenol Red- ⁇ -D-galactopyranoside
  • CPRG yellow chlorophenol Red- ⁇ -D-galactopyranoside
  • chitinase is used as an alternative colorimetric reporter enzyme, which cleaves the colorless 4-Nitrophenyl N,N′-diacetyl-beta-D-chitobioside substrate to a yellow p-nitrophenol product ( FIG. 9 )
  • RNA sensors can be used to detect RNAs of interest in a sample, and optionally quantitate the RNA level.
  • RNAs of interest include, but are not limited to, antibiotic resistance genes, and mRNAs that encode proteins of interest.
  • reaction regions host the same sensors, and thus a plurality of samples can be tested for the same analyte.
  • reaction regions host different sensors, and thus a plurality of analytes can be detected on the same support or substrate.
  • the same reaction region can host one or more different sensors.
  • the analyte can be a gas molecule, a small molecule, a nucleic acid, a protein, a peptide, a pathogen, a pathogen extract, a metabolite, an antibiotic drug, an explosive chemical, a toxic chemical, or an industrial chemical.
  • An industrial chemical can be a process by-product such as cellobiose, an intermediate in fuel production, or a bioreactor product such as vitamins.
  • the analyte can be a solid, liquid or gas. In one embodiment, the analyte is a heavy metal. In one embodiment, the analyte is an insecticide residue.
  • the analyte can be from a variety of samples, including, but not limited to, a biological sample, an environmental sample, a culture sample, an industry sample (e.g., biofuel production).
  • sensors producing fluorescent signals it would be apparent to a skilled artisan that any commercial or homemade device or system that can detect fluorescence can be used for the purpose of detecting the signals, including, but not limited to, a microscope, a fluorescence microplate reader, and a fluorescence spectrometer.
  • human eyes can detect the signals within the visible spectrum, which is from about 390 nm to 700 nm.
  • a commercial or homemade device that can detect colorimetric signals can be used as well, including, but not limited to a camera and a microscope.
  • sensors producing electronic signals it would be apparent to a skilled artisan that any commercial or homemade device or system that can measure electronic signals can be used for the purpose of detecting the signals.
  • Exemplary devices or systems include a multimeter, an ohmmeter, a voltmeter, an ammeter, and an oscilloscope.
  • an automatic device or system can permit continuous monitoring and significantly increase the detection throughput.
  • the senor can detect temperature, pressure, humidity, light intensity, light spectrum, or a combination thereof.
  • the synthetic gene network comprises a logic circuit, and thus can perform one or more logic functions upon activation.
  • a logic circuit In the field of synthetic biology, significant progress has been made in designing and assembling biological components into logic circuits that can mimic or even outperform electronic circuits, resulting in the creation of a large variety of logic circuits. See WO2014093852 for examples.
  • the logic circuit can be activated by contacting the logic circuit with water.
  • the logic circuit can be activated by contacting the logic circuit with water and a composition comprising one or more triggers.
  • a composition comprising one or more triggers.
  • an AND gate is one of the most basic logic circuits, requiring the simultaneous presence of two appropriate triggers in order for the AND gate to turn on. If only one of the triggers is present, the AND gate would not turn on.
  • the trigger can comprise temperature, pressure, humidity, light intensity, light spectrum, an electrical current, a voltage, a chemical element, an ion, a small molecule, a peptide, a protein, a nucleic acid, an extract, or a combination thereof.
  • signal produced by a sensor described herein can serve as a component in a logic circuit.
  • proteins lyophilized into the reaction regions or proteins expressed by a template-directed synthetic reaction can form a logic function or a portion thereof.
  • the shelf-stable composition can be doped by a variety of proteins.
  • the shelf-stable composition further comprises a repressor protein.
  • the repressor protein can improve the performance of some synthetic gene networks.
  • the repressor protein can prevent or reduce the probability of a reporter component producing a signal absent of an analyte.
  • the repressor protein is a transcription repressor.
  • the shelf-stable composition further comprises an amplification system.
  • the amplification system comprises, e.g., a set of reagents sufficient for the amplification of nucleic acids (e.g., RNA or DNA).
  • nucleic acids e.g., RNA or DNA
  • the target RNA can be amplified prior to its detection, thus resulting in better signal-over-noise ratio.
  • the amplification is isothermal amplification (see, e.g., Yan et al., Molecular BioSystems, 2014, 10, 970-1003).
  • the amplification system comprises the DNA polymerase Phi 29. Information regarding the use of Phi29 for amplification is disclosed, for example, in Dean et al., Genome Research, 2001, 11, 1095-1099.
  • Lyophilization also known as freeze-drying, is a dehydration process that involves freezing a material and then reducing the surrounding pressure to allow water to sublimate. Parameters such as freezing temperature, rate of temperature change, and pressure are variables for different lyophilization process. Accordingly, the lyophilization processes used in the methods and compositions herein are not limited to a specific set of parameters. It should be apparent to a skilled artisan that preferred lyophilization processes would yield a shelf-stable composition with a long shelf life. Once the synthetic gene networks and/or cell-free systems are frozen, they should be kept frozen, i.e., prevented from thawing, until the application of low pressure (e.g., vacuum).
  • low pressure e.g., vacuum
  • the material can have large heat capacity.
  • the frozen synthetic gene networks and/or cell-free systems are substantially shielded from light during the lyophilization process. This is particularly useful for protecting components sensitive to light.
  • the shelf-stable composition is produced by a process comprising contacting a solid support with an aqueous solution comprising a cell-free system and a synthetic gene network, and lyophilizing said solid support.
  • the composition when stored at room temperature (i.e., about 20° C. to 24° C.) and relative humidity of no more than 10%, the composition has a shelf life of at least two weeks, at least one month, at least two months, or at least six months.
  • the compositions described herein can function at room temperature.
  • the temperature at which the compositions function is about 37° C.
  • the use of thermostable enzymes permits the use of temperatures above 37° C.
  • compositions described herein can function when a certain temperature threshold is reached.
  • the temperature threshold is about 37° C.
  • thermostable enzymes permits the use of temperatures above 37° C.
  • an engineered signaling pathway can be lyophilized on a solid support; a solution comprising a kinase can be used to activate the pathway and amplify input.
  • engineered signaling pathway There are two main types of engineered signaling pathway: those that rewire existing signal transduction pathways, and those that create artificial signaling modules. More details about engineered signaling pathways can be found, for example, in Kiel et al., Cell 2010, 140, 33-47, and Grubelnik et al., Biophysical Chemistry 2009, 143, 132-138, the contents of each of which are incorporated herein by reference in their entirety.
  • a related aspect of the methods and compositions described herein relates to a shelf-stable composition comprising a lyophilized synthetic gene network.
  • the shelf-stable composition is a powder, which can be in any of a variety of containers.
  • the lyophilized synthetic gene network can be in a container such as a tube, a bottle, or a vial.
  • the shelf-stable composition a lyophilized synthetic gene network can be rehydrated to form a solution.
  • the disclosed technology also intends to encompass any intermediate product produced in the lyophilization process.
  • the disclosed technology encompasses frozen cell-free systems and/or synthetic biological circuits (e.g., synthetic gene networks), which can become active upon thawing.
  • one aspect regards a method of detecting an analyte, comprising providing a shelf-stable composition as described herein, wherein the composition comprises a sensor as described herein, contacting the composition with the analyte in the presence of water, and detecting a signal, wherein detection of the signal indicates the presence of the analyte.
  • the method further comprises a step of preventing or slowing water evaporation.
  • the step comprises contacting the composition with a barrier to water evaporation.
  • the barrier is a physical barrier including, but not limited to, a tape, a film, a glass slide, a cover, and a solution that is immiscible with water (e.g., oil).
  • the step comprises enclosing the composition in an enclosure that limits evaporation of water.
  • the synthetic gene networks and cell-free systems In order to produce a detectable signal, the synthetic gene networks and cell-free systems generally require an incubation period. Incubation at a given temperature (often, e.g., 37° C.) can proceed on the order of seconds, minutes, or hours, depending upon the exact system. As noted in the Examples herein, in some embodiments, the reaction continues to generate a product or signal with continuing incubation, permitting the generation of a reaction curve for accumulation of signal.
  • a given temperature often, e.g. 37° C.
  • the reaction continues to generate a product or signal with continuing incubation, permitting the generation of a reaction curve for accumulation of signal.
  • the method produces a qualitative output (e.g., positive or negative).
  • a positive output means that the analyte is detected, while a negative output means that the analyte is not detected.
  • the method produces a quantitative output.
  • quantitative is used herein to also encompass semi-quantitative.
  • quantification can be done by comparing a signal produced by a sensor against a negative control and then quantifying the signal intensity vs. time.
  • a control reaction or a set of control reactions with varying known amounts of analyte can serve to provide quantitation of analyte in an unknown sample.
  • an inert RNA can be used to define a threshold for the RNA sensor.
  • Another aspect of the technology disclosed herein regards a method of activating a synthetic gene network lyophilized on a solid support, comprising providing a shelf-stable composition as described herein, wherein the composition comprises the synthetic gene network, and contacting the composition with water or an aqueous sample.
  • a related aspect of the technology disclosed herein regards a method of activating a lyophilized synthetic gene network, the method comprising providing a lyophilized cell-free system comprising components sufficient for a template-directed synthetic reaction, and contacting the lyophilized synthetic gene network with the lyophilized cell-free system in the presence of water.
  • kits comprising a shelf-stable composition as described herein and packaging materials thereof.
  • the kit further comprises an enclosure, wherein said enclosure encloses the composition during a template-directed synthetic reaction to slow or prevent water evaporation.
  • described herein is a paper-based synthetic gene network in a reader or a detection device, wherein the reader or detection device detects a signal produced by the synthetic gene network.
  • the paper-based synthetic gene network is disposed on a support during the detection.
  • paper-based transcription and/or translation reactions can be used to host nucleic acid-based sensor programs.
  • these components are used to build devices that can detect, for example, the presence of pathogens and environmental contaminants, as well as measure other parameters of patient physiology, the chemical environment, and biological signals from the environment.
  • proteins synthesized using the compositions described herein are properly folded, as evidenced by fluorescent proteins that rely on their properly folded structure for fluorescence (e.g., GFP, mCherry, Cerulean, or Venus).
  • fluorescent proteins e.g., GFP, mCherry, Cerulean, or Venus.
  • proteins with enzymatic activity e.g., Beta-galactosidase or Chitinase
  • proteins with enzymatic activity e.g., Beta-galactosidase or Chitinase
  • proteins with enzymatic activity e.g., Beta-galactosidase or Chitinase
  • Such proteins can be produced in sufficient quantity to modify substrates (e.g., CPRG or Chitin).
  • molecular tools capable of performing tasks e.g., RNA toehold switches or the FRET-based nanosensor
  • compositions and methods described herein also offer a new venue for synthetic biology at large. Beyond in vitro diagnostics, the compositions and methods described herein provide a much-needed medium for the commercialization of synthetic biology. This approach can permit the straightforward, sterile and abiotic distribution of synthetic biology-based technology to clinical settings, food processing and industry, the military and consumer products. This could encompass embedding sensors, counters and timers and other synthetic gene networks into products, as well as tools for molecular manufacturing. Examples of the latter include the on-demand, on-site manufacturing of pharmaceuticals, therapeutic proteins and other biomolecules or biomaterials.
  • a virus can be synthesized using the compositions and/or methods described herein.
  • the virus is a non-enveloped virus.
  • Non-enveloped virus can come from families including, but not limited to, Adenoviridae (e.g., adenovirus, infectious canine hepatitis virus), Papovaviridae (e.g., papillomavirus, polyomaviridae, simian vacuolating virus), Parvoviridae (e.g., parvovirus B19, canine parvovirus), Anelloviridae (e.g., torque teno virus), Caulimoviridae (e.g., cauliflower mosaic virus), Myoviridae, Phycodnaviridae, Tectiviridae, Circoviridae, Reoviridae (e.g., Reovirus, rotavirus), Picornaviridae (e.g., Enterovirus,
  • Adenoviridae
  • a freeze-dried composition comprising a cell-free system and a set of nucleic acids encoding an appropriate set of proteins (e.g., capsids) of the virus of interest can be used.
  • proteins e.g., capsids
  • the freeze-dried composition is activated, e.g., by the addition of water, proteins can be synthesized in vitro and then self-assemble to form the virus.
  • the virus When incorporated into a wound dressing, topical preparation, or implantable device or preparation, the virus would be assembled at the site of application. This can permit, e.g., viral vector production at the site of need or simply in an individual in an on-demand manner.
  • compositions and methods for virus synthesis can be used therapeutically, e.g., for transient gene therapy, e.g., delivery of adenovirus.
  • nucleic acids can encode the viral protein component(s) necessary for self-assembly/packing of a viral genome construct carrying a therapeutic or cargo coding sequence of interest.
  • the genomic construct is packaged and will be delivered to host cells upon infection.
  • the assembled virus particles may not be infective and, for instance, can be used as vaccine antigens, nanoparticles, or biomaterials.
  • the freeze-dried compositions and methods for virus synthesis can be used in a research setting, e.g., for the delivery of viral expression constructs to mammalian cells. Many small aliquots of viruses can be produced in this manner for high-throughput screening.
  • the freeze-dried compositions and methods for virus synthesis can also be used in vaccine production for viruses or other microbial agents, such as rotavirus.
  • viral proteins can be expressed simply as antigens without the formation of capsids, as in vaccines for HPV (Human papillomavirus), and DTaP (Diphtheria, Tetanus, and Pertussis), among a great many others.
  • the virus is a bacteriophage.
  • the freeze-dried compositions and methods for bacteriophage synthesis can be used in a research setting, e.g., for the delivery of genes to bacterial cells.
  • the freeze-dried compositions and methods for bacteriophage synthesis can also be used in therapeutic applications, e.g., phage therapy.
  • the freeze-dried compositions and methods for bacteriophage synthesis can also be used in diagnostic applications, e.g., for the detection of pathogens.
  • a therapeutic protein in one embodiment, can be synthesized using the compositions and/or methods described herein.
  • a freeze-dried composition comprising a cell-free system and a nucleic acid encoding the protein of interest can be used.
  • the freeze-dried composition can further comprise a synthetic gene network that can actuate the protein synthesis in response to an input or stimulus (e.g., a pathogen, an oncoprotein, a cytokine, a hormone, etc.).
  • therapeutic proteins include, but are not limited to human amylin, insulin, growth hormone (GH), mecasermin, erythropoietin, darbepoetin- ⁇ , granulocyte colony stimulating factor, pegfilgrastim, granulocyte-macrophage colony stimulating factor, human follicle-stimulating hormone, human chorionic gonadotropin, lutropin- ⁇ , cytokines (e.g., interferons such as interferon alfacon 1, interferon- ⁇ 2a), aldesleukin, Hepatitis B surface antigen (HBsAg), HPV protein vaccine, OspA, and antimicrobial peptides. See Leader et al., Nature 2008, 7, 21-39 for more examples of therapeutic proteins that can be genetically expressed or produced according to the methods described herein.
  • GH growth hormone
  • mecasermin erythropoietin
  • darbepoetin- ⁇ granulocyte colony stimulating
  • the therapeutic protein is an antibody or an antigen-binding fragment thereof.
  • therapeutic antibodies include, but are not limited to, bevacizumab, cetuximab, panitumumab, alemtuzumab, rituximab, trastuzumab, abatacept, infliximab, enfuvirtide, crotalidae, and ranibizumab.
  • the antibody or fragment thereof can be linked to a drug (e.g., a chemotherapeutic drug) for targeted delivery. Production of antibodies or fragments thereof can also be used in a research setting.
  • the therapeutic protein is an enzyme, e.g., phenylalanine hydroxylase for the treatment of phenylketonuria.
  • components for a drug synthesis pathway can be synthesized using the compositions and/or methods described herein.
  • the components for a drug synthesis pathway can convert an inactive bioprecursor pro-drug to a bioactive form. Indeed, even expression of a single enzyme in a spatially or temporally restricted manner permitted by the on-demand manufacture of proteins as described herein can be used to convert a pro-drug to an active drug in a user-regulated way.
  • a pro-drug is peptide-appended therapeutics, which can be activated by proteolytic cleavage of the peptide moiety. In such cases, therapeutics can be released from engineered materials in wound dressings by expressed proteases.
  • the drug synthesis pathway can be a pathway that converts a stable, inexpensive precursor to a drug, e.g., cholesterol to steroid, or amorphadiene to artemisinin, which is used to treat malaria.
  • nanoparticles can be synthesized using the compositions and/or methods described herein.
  • a freeze-dried composition comprising a cell-free system and a nucleic acid encoding a metal-binding protein can be used.
  • the metal-binding protein can facilitate the synthesis of nanoparticles of interest. See for example, Lee et al., ACS Nano 2012, 6, 6998-7008.
  • nanoparticles include, but are not limited to, quantum dots, metal nanoparticles such as gold or iron nanoparticles.
  • oligonucleotides can be synthesized using the compositions and/or methods described herein.
  • the oligonucleotides synthesized undergo folding and/or self-assembling to form DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) origami construct.
  • DNA deoxyribonucleic acid
  • RNA ribonucleic acid
  • DNA origami constructs and new strategies increasing the in vivo stability of such constructs are being developed for their use in therapeutics. See, for example, Douglas et al., Science 2012, 335, 831-834.
  • the expression of the desired product can be made sensitive to the presence of another molecule or agent by integrating a synthetic gene network that acts as a sensor into the design.
  • the desired gene product is only made when the molecule or agent is present, and that agent can be, e.g., a pathogen, a metabolite, a protein, or even a small molecule administered separately.
  • the technology disclosed herein can provide an excellent platform for DNA/RNA-based computing and logic reactions.
  • a paper/electronic interface was developed that can sense computational output and the response of embedded biosensors. This can permit automation and allow for multiplexed arrays of reactions.
  • transcription reactions can express RNAs that then interact with a network of catalytic nucleic acids, which can be used in signal amplification.
  • the cell extracts used to supply the transcription and translation machinery also offer a unique opportunity for molecular biologists to work with organisms that are difficult to culture.
  • nucleic acid-based sensors can be designed to directly detect one or more orthogonal, species-specific RNAs.
  • This sequence-based method of detection means that tools can be designed rationally, lowering development costs and allowing for a short design to production cycle.
  • the sequence-based sensors also permit the acquisition of other relevant clinical information, such as the presence of drug-resistance genes or other indicators of pathogenesis, such as biofilm-specific RNAs. Thresholding of the nucleic acid-based sensors also allows for semi-quantitative diagnostics, a much needed feature that is for the most part not available with RDTs (Michael S. Cordray and Rebecca R. Richards-Kortum, Am. J. Trop. Med. Hyg., 2012, 87, 223-230).
  • quantification can be done without thresholding. For example, see FIG. 26 , where a linear relationship exists for RNA concentration in the range of 0-2 ⁇ M.
  • the sensors described herein are also less expensive than most of the standard of care options currently available. At the moment, the cost per sensor as described herein is between about 35 ⁇ -60 ⁇ using commercial cell-free systems. However, these systems can be readily produced in house, reducing the cost to as little as 4 ⁇ per sensor (http://www.openwetware.org/wiki/Biomolecular_Breadboards:Protocols:cost_estimate). This compares to $0.45-$1.40 for a single RDT reaction and $1.50-$4.00 (reagents only) for PCR (Michael S. Cordray and Rebecca R. Richards-Kortum, Am. J. Trop. Med. Hyg. 2012, 87, 223-230).
  • compositions and methods described here are also competitive with regard to how long it takes to make a positive identification.
  • the sensors described herein can yield positive results in as little as 25 minutes depending on the sensor format, with most sensors functioning with a reaction time of under an hour. This compares to RDTs, which can detect a single antigen in ⁇ 20 minutes or PCR, which can take 1.5 to 2 hours and is largely confined to laboratory settings.
  • paragraph 1 A shelf-stable composition comprising a cell-free system comprising components sufficient for a template-directed synthetic reaction, wherein said cell-free system is lyophilized on a porous substrate and is substantially free of water, and wherein said cell-free system is active for said template-directed synthetic reaction upon re-hydration. paragraph 2.
  • paragraph 3 The shelf-stable composition of paragraph 2, wherein said synthetic gene network comprises nucleic acids.
  • paragraph 4 The shelf-stable composition of paragraph 3, wherein said nucleic acid comprises DNA, RNA, an artificial nucleic acid analog, or a combination thereof. paragraph 5.
  • the shelf-stable composition of any of paragraphs 1 to 4, wherein said template-directed synthetic reaction is a translation reaction.
  • paragraph 7. The shelf-stable composition of any of paragraphs 1 to 4, wherein said template-directed synthetic reaction is a coupled transcription and translation reaction.
  • paragraph 8. The shelf-stable composition of paragraph 1, wherein said components are sufficient for a transcription reaction, and comprise promoter-containing DNA, RNA polymerase, ribonucleotides, and a buffer system.
  • paragraph 9 The shelf-stable composition of paragraph 1, wherein said components are sufficient for a translation reaction, and comprise ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system. paragraph 10.
  • the shelf-stable composition of paragraph 1 wherein said components are sufficient for a coupled transcription and translation reaction, and comprise promoter-containing DNA, RNA polymerase, ribonucleotides, ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system. paragraph 11.
  • said porous substrate comprises paper, quartz microfiber, mixed esters of cellulose, porous aluminum oxide, or a patterned surface.
  • paragraph 12. The shelf-stable composition of any of paragraphs 1 to 11, wherein said porous substrate is pre-treated with bovine serum albumin, polyethylene glycol, Tween-20, Triton-X, milk powder, casein, fish gelatin, or a combination thereof. paragraph 13.
  • paragraph 15. The shelf-stable composition of paragraph 13, wherein the recombinant protein transcription/translation system is reconstituted from purified components necessary for E. coli translation.
  • paragraph 16 The shelf-stable composition of any of paragraphs 2 to 15, wherein said synthetic gene network functions as a sensor. paragraph 17.
  • the shelf-stable composition of paragraph 16 wherein said sensor can detect the presence of an analyte in an aqueous sample. paragraph 18.
  • paragraph 19 The shelf-stable composition of paragraph 17, wherein detection of said analyte produces an electronic signal.
  • paragraph 20 The shelf-stable composition of any of paragraphs 2 to 15, wherein said synthetic gene network comprises a logic circuit.
  • paragraph 23. The shelf-stable composition of paragraph 22, wherein said trigger is selected from the group consisting of a chemical element, a small molecule, a peptide, a protein, a nucleic acid, an extract, and a combination thereof.
  • paragraph 24. The shelf-stable composition of any of paragraphs 1 to 23, characterized in that the shelf-stable composition is shelf stable for at least two weeks. paragraph 25.
  • a shelf-stable composition comprising a cell-free system comprising components sufficient for a template-directed synthetic reaction, a synthetic gene network, and a solid support, wherein said shelf-stable composition is substantially free of water, and wherein said cell-free system is active for said template-directed synthetic reaction upon rehydration.
  • said synthetic gene network comprises nucleic acids.
  • said nucleic acid comprises DNA, RNA, an artificial nucleic acid analog, or a combination thereof.
  • paragraph 28. The shelf-stable composition of any of paragraphs 25 to 27, wherein said template-directed synthetic reaction is a transcription reaction. paragraph 29.
  • paragraph 30. The shelf-stable composition of any of paragraphs 25 to 27, wherein said template-directed synthetic reaction is a coupled transcription and translation reaction.
  • paragraph 31. The shelf-stable composition of paragraph 25, wherein said components are sufficient for a transcription reaction, and comprise promoter-containing DNA, RNA polymerase, ribonucleotides, and a buffer system.
  • paragraph 32. The shelf-stable composition of paragraph 25, wherein said components are sufficient for a translation reaction, and comprise ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system. paragraph 33.
  • paragraph 34 The shelf-stable composition of any of paragraphs 25 to 33, wherein said solid support comprises paper, quartz microfiber, mixed esters of cellulose, porous aluminum oxide, a patterned surface, a tube, a well, or a chip. paragraph 35.
  • the shelf-stable composition of paragraph 36 wherein the recombinant protein transcription/translation system is reconstituted from purified components necessary for E. coli translation.
  • paragraph 39 The shelf-stable composition of any of paragraphs 25 to 38, wherein said synthetic gene network functions as a sensor.
  • paragraph 40. The shelf-stable composition of paragraph 39, wherein said sensor can detect the presence of an analyte in an aqueous sample.
  • paragraph 41. The shelf-stable composition of paragraph 40, wherein detection of said analyte produces an optical signal.
  • paragraph 42. The shelf-stable composition of paragraph 40, wherein detection of said analyte produces an electronic signal.
  • paragraph 43 The shelf-stable composition of any of paragraphs 25 to 38, wherein said synthetic gene network comprises a logic circuit.
  • paragraph 44 The shelf-stable composition of paragraph 43, wherein said logic circuit comprises an AND gate, a NOT gate, an OR gate, a NOR gate, a NAND gate, a XOR gate, a XAND gate, or a combination thereof.
  • paragraph 45 The shelf-stable composition of paragraph 43 or 44, wherein said logic circuit is activated upon contacting said shelf-stable composition with water and a composition comprising a trigger.
  • paragraph 46 is selected from the group consisting of a chemical element, a small molecule, a peptide, a protein, a nucleic acid, an extract, and a combination thereof. paragraph 47.
  • the shelf-stable composition of any of paragraphs 25 to 46 characterized in that the shelf-stable composition is shelf stable for at least two weeks.
  • paragraph 48 A shelf-stable composition produced by contacting a solid support with an aqueous solution comprising a cell-free system and a synthetic gene network, and lyophilizing said solid support.
  • paragraph 49 A method of detecting an analyte, comprising (i) providing a composition of any of paragraphs 1 to 47, wherein said composition comprises a nucleic acid-based sensor; (ii) contacting said composition with said analyte in the presence of water; and (iii) detecting a signal, wherein detection of said signal indicates the presence of said analyte. paragraph 50.
  • paragraph 49 further comprising a step of contacting said composition with a barrier to water evaporation or enclosing said composition in an enclosure after step (ii).
  • paragraph 51 The method of paragraph 49 or 50, wherein said method provides a measure of the amount of said analyte.
  • paragraph 52 The method of any of paragraphs 49 to 51, wherein said nucleic acid comprises DNA, RNA, an artificial nucleic acid analog, or a combination thereof.
  • paragraph 53 The method of any of paragraphs 49 to 52, wherein said nucleic acid-based sensor comprises a reporter gene.
  • paragraph 54 The method of paragraph 53, wherein said reporter gene encodes a fluorescence protein, an enzyme, or an antigen. paragraph 55.
  • nucleic acid-based sensor comprises a catalytic nucleic acid.
  • paragraph 56 The method of any of paragraphs 49 to 52, further comprising providing a fluorophore, whereby said fluorophore can couple to a nucleic acid to produce a change in fluorescence.
  • paragraph 57 The method of any of paragraphs 49 to 56, wherein said analyte is selected from the group consisting of a nucleic acid, a pathogen, a pathogen extract, a metabolite, an antibiotic drug, an explosive chemical, a toxic chemical, and an industrial chemical.
  • paragraph 58 The method of paragraph 57, wherein said toxic chemical is a heavy metal or insecticide residue. paragraph 59.
  • paragraph 60 The method of any of paragraphs 49 to 58, wherein said signal is an optical signal.
  • paragraph 60 The method of paragraph 59, wherein said optical signal is luminescence.
  • paragraph 61 The method of paragraph 59, wherein said optical signal is fluorescence.
  • paragraph 62 The method of paragraph 59, wherein said optical signal is a visible color.
  • paragraph 63 The method of any of paragraphs 49 to 58, wherein said signal is an electronic signal.
  • paragraph 64 The method of any of paragraphs 49 to 63, wherein the analyte is in an aqueous solution.
  • paragraph 65 A kit comprising a shelf-stable composition of any of paragraphs 1 to 47 and packaging materials thereof. paragraph 66.
  • paragraph 65 further comprising an enclosure, wherein said enclosure encloses said composition during a template-directed synthetic reaction to slow or prevent water evaporation.
  • paragraph 67 A method of activating a synthetic gene network lyophilized on a porous substrate, comprising: (i) providing a shelf-stable composition of any of paragraphs 1 to 47, wherein said composition comprises said synthetic gene network; and (ii) contacting the composition with a solution comprising water.
  • paragraph 68 The method of paragraph 67, wherein said synthetic gene network functions as a sensor, and wherein said solution further comprises an analyte capable of activating said sensor. paragraph 69.
  • paragraph 68 wherein said analyte is selected from the group consisting of a nucleic acid, a pathogen, a pathogen extract, a metabolite, an antibiotic drug, an explosive chemical, a toxic chemical, and an industrial chemical.
  • paragraph 70 The method of paragraph 67, wherein said synthetic gene network comprises a logic circuit, and wherein said solution further comprises a trigger capable of activating said logic circuit.
  • a method of activating a lyophilized synthetic gene network comprising (i) providing a lyophilized cell-free system comprising components sufficient for a template-directed synthetic reaction; and (ii) contacting said lyophilized synthetic gene network with said lyophilized cell-free system in the presence of water.
  • paragraph 73. A method of stabilizing a synthetic gene network, comprising lyophilizing said synthetic gene network. paragraph 74. The method of paragraph 73, wherein said synthetic gene network is on a solid support during lyophilization. paragraph 75. The method of paragraph 74, wherein the solid support is paper.
  • paragraph 76. A shelf-stable composition of any of paragraphs 1 to 47 and a reader, wherein said reader can measure a signal from said shelf-stable composition. paragraph 77.
  • a shelf-stable composition comprising a lyophilized synthetic biological circuit.
  • paragraph 78. The shelf-stable composition of paragraph 77, wherein the synthetic biological circuit is lyophilized on a porous substrate.
  • paragraph 79. The shelf-stable composition of paragraph 77 or 78, wherein the synthetic biological circuit is a synthetic gene network.
  • paragraph 80. The shelf-stable composition of paragraph 79, further comprising a cell-free system.
  • the present invention relates to the herein described compositions, methods, and respective component(s) thereof, as essential to the invention, yet open to the inclusion of unspecified elements, essential or not (“comprising”).
  • other elements to be included in the description of the composition, method or respective component thereof are limited to those that do not materially affect the basic and novel characteristic(s) of the invention (“consisting essentially of”). This applies equally to steps within a described method as well as compositions and components therein.
  • the inventions, compositions, methods, and respective components thereof, described herein are intended to be exclusive of any element not deemed an essential element to the component, composition or method (“consisting of”).
  • freeze-dried cell extracts can support the constitutive expression of GFP, via E. coli RNA polymerase or T7 RNA polymerase based promoters ( FIG. 1A ).
  • the later T7-based expression can also be supported by freeze drying a recombinant protein-based system. These results essentially reflect the expression levels observed in fresh cell-free reactions and in E. coli .
  • the freeze dried cell-free systems are stable over time with transcription and translation activity remaining high after months of room temperature storage ( FIG. 1B ).
  • Inducible expression systems were used for synthetic gene networks. Using the classic inducible tetO promoter, induced by the antibiotic doxycycline or chemical analogs, GFP expression was readily induced.
  • tight regulatory control in vitro required that cell extracts be supplemented with tet repressor (tetR) protein to prevent reporter leakage prior to repressor expression from a constitutive tetR element in the gene circuit ( FIG. 8A ).
  • tetR tet repressor
  • RNA-inducible riboswitches For the inducible regulation of the potent T7 promoter, a new generation of RNA-inducible riboswitches, called toe-hold switches, is chosen. These robust switches provided tight, almost complete, regulation over the T7 transcripts, with GFP only being produced in the presence of the correct RNA trigger ( FIGS. 10A-10C ).
  • Paper previously used in chemistry-based diagnostics (Martinez et al., Angew. Chem. Int. Ed., 2007, 46, 1318-1320), serves as a high capillary matrix that evenly distributes small volume reactions and provides a surface for the display of gene circuit outputs. It was found that first treating the paper with BSA or other similar blocking reagents significantly improved the output of expression constructs ( FIG. 11A ). Small 2 mm filter paper discs were freeze dried with cell-free systems to produce GFP from either E. coli RNA polymerase or T7 polymerase-based expression plasmids.
  • the lyophilized sensors can be designed to produce a colorimetric output visible to the naked eye.
  • GFP was replaced with the enzyme beta-galactosidase or LacZ to produce a system that generates a dramatic color change in response to the presence of synthetic trigger RNA.
  • LacZ leads to the enzymatic cleavage of yellow chlorophenol Red- ⁇ -D-galactopyranoside substrate to magenta chlorophenol red.
  • an enzyme-mediated reporter introduces an additional signal amplification step into the system. Using the PA toe-hold switch, the response time of the reaction can be seen to begin at the 25 minute time point in the time series that documents the reaction on paper ( FIG. 7E ).
  • Lyophilized sensors can be designed to detect sequences within full-length active mRNA targets, a key feature for a diagnostics platform.
  • the first goal was the detection of GFP and mCherry mRNA.
  • sensors were built to target sequences likely to be accessible, and, when tested, yielded fluorescent induction in the presence of GFP (60-fold) and mCherry (14-fold) mRNAs, respectively ( FIGS. 12A-12B ).
  • FIGS. 12A-12B As a demonstration of the potential for paper-based synthetic gene networks as an in vitro diagnostics platform, mRNA sensors for antibiotic resistance genes were next developed.
  • mRNA sensors for ampicillin (15-fold), kanamycin (6-fold), chloramphenicol (20-fold) and spectinomycin (32-fold) yielded significant GFP fold-change in the presence of their respective mRNAs ( FIG. 13A ).
  • These sensors were modified to produce LacZ, which in the presence of mRNA from respective antibiotic resistance genes converted sensor output into the visible colorimetric mode ( FIG. 13B ).
  • Bacterial and mammalian components can be freeze-dried onto paper, and other porous substrates, to create poised synthetic gene networks that are stable for long-term storage at room temperature and can be activated by rehydration.
  • the resulting engineered materials have the transcription and translation properties of a cell and can host genetically encoded tools using, e.g., commercially available cell-free transcription and translation systems.
  • the technology is demonstrated herein with small molecule and RNA actuation of genetic switches, the construction of paper-based sensors for glucose and mRNAs, including antibiotic resistance genes, and the characterization of novel gene circuits.
  • gene circuits can be enhanced with colorimetric outputs for detection by the naked eye, as well as with the fabrication of a low cost, electronic optical interface for quantification and possible automation of reactions.
  • These low cost, paper-based synthetic gene networks have the potential to bring bio-based sensors, counters, timers and simple logic to portable devices.
  • Small 2 mm filter paper discs were freeze-dried with bacterial cell-free systems (1.8 ⁇ L) containing either E. coli (S30) or T7 RNAPs (S30 T7, PT7) and a corresponding GFP expression plasmid ( FIG. 16D ). Upon rehydration and incubation at 37° C., these paper-based reactions yielded consistent GFP fluorescence under the regulation of either RNAP. Fluorescence imaging of the paper discs confirm GFP expression, and reaction dynamics were monitored by placing the paper discs at the bottom of black, clear bottom 384 well plates for incubation in a 37° C. plate reader ( FIG. 16E ).
  • TetO regulated expression a classic synthetic biology switch, was used. Regulation of this system is mediated by the tet repressor (tetR), that binds to the TetO promoter, preventing transcription ( FIG. 16F , Lutz R, Bujard H., Nucleic Acids Res. 1997, 25:1203-10).
  • tetR tet repressor
  • FIG. 16F Lutz R, Bujard H., Nucleic Acids Res. 1997, 25:1203-10.
  • Such regulation performed in vitro required that constitutive tetR expression also be encoded into the synthetic gene network. Expression is then induced by addition of the antibiotic doxycycline or chemical analogs (aTc), which disrupts tetR binding to the promoter, allowing transcription of the regulated gene.
  • aTc antibiotic doxycycline or chemical analogs
  • Freeze-dried discs were prepared with a cell-free system containing S30 E. coli cell extract, pre-translated tetR, and the network elements encoding the constitutive expression of tetR and TetO regulated GFP or mCherry. Varying only the presence of aTc, discs were rehydrated and incubated at 37° C. for 2 hours. The aTc-induced discs yielded expression of GFP and mCherry at 5 and 32-fold, respectively ( FIG. 16G ; FIG. 21 ).
  • RNA-actuated gene circuits An important trend for synthetic biology is the use of RNA-actuated gene circuits (Callura, J. M., et al., Proc Natl Acad Sci USA 2012, 109, 5850-5855). Unlike circuits based on small molecule-based regulation, which are limited by the number of available unique recognition domains, RNA-based switches can be rationally programmed to recognize sequence-specific triggers and accordingly have the potential to offer essentially unlimited signaling space (Callura, J. M., et al., Proc Natl Acad Sci USA 2010, 107, 15898-15903; Isaacs, F. J., et al., Nat Biotechnol 2004, 22, 841-847; Lucks, J.
  • toehold switches Green et al., 2014
  • T3 RNAP alternative RNA polymerases
  • Toehold switch plasmids were constructed using conventional molecular biology techniques. Synthetic DNA templates (Integrated DNA Technologies, Inc.) were amplified using PCR, inserted into plasmids using Gibson assembly (Gibson et al., Nat. Methods 2009, 6, 343-345) with 30-bp overlap regions, and then successfully constructed plasmids identified using DNA sequencing. All plasmids were derived from pET system parent plasmids (EMD Millipore) and constitutively express lad and antibiotic resistance genes. Additional descriptions of the toehold switch plasmids and their sequences are provided in Green et al. (Green et al., Cell 2014).
  • the paper-based system was designed to produce a colorimetric output visible to the naked eye.
  • GFP was replaced with the enzyme ⁇ -galactosidase (LacZ) to produce a system that generates a dramatic enzyme-mediated color change in response to conditional inputs to synthetic gene networks ( FIG. 18A ).
  • LacZ cleaves the yellow substrate, chlorophenol Red- ⁇ -D-galactopyranoside, embedded into the freeze-dried paper discs, to produce a magenta chlorophenol red product.
  • chitinase An alternative colorimetric reporter enzyme, chitinase, was also incorporated into synthetic gene networks for systems based on extracts from cells that contain a lacz background. As demonstrated with the teto_chitinase switch, the presence of atc inducer results in the expression of chitinase, which cleaves a colorless substrate (4-nitrophenyl n,n′-diacetyl-beta-d-chitobioside) to yield a yellow p-nitrophenol product. The colorimetric output is visible to the naked eye and can be quantified using a plate reader utilizing absorbance (410 nm; FIG. 33 ). Color development with this system was linear from the onset of detectable output at about 60 min, until the end of the experiment at 800 min, with a maximum induction of 38-fold at 420 min.
  • a low-cost electronic optical reader was built to permit quantification, and ultimately, automation of the paper-based reactions. Such a device could also impart these molecular devices with the ease of use and convenience of a home glucose monitor.
  • LacZ-based toehold switches on paper discs were placed between LED light sources (570 nm) and electronic sensors ( FIG. 18H ). In the event of a positive reaction, light transmission is progressively blocked by the production of the purple LacZ cleavage product. LEDs and sensors were coordinated through multiplexers connected to an electrician that controlled the read pattern and rate parameters.
  • Electronic hardware was housed using computer-designed parts laser cut from acrylic, to create a device for under $100 USD ( FIG. 18H ).
  • Freeze-dried paper discs were placed into holes on a chip, rehydrated, incubated within the device at 37° C. and monitored in real-time through an attached laptop. As a proof-of-concept, the G_LacZ toehold switch was tested, and consistent and significant reads from different concentrations of RNA trigger were observed ( FIG. 18I ).
  • toehold switch sensors capable of detecting full-length active mRNA targets were developed, a desirable feature for a diagnostics platform.
  • the first goal was the detection of GFP and mCherry mRNA.
  • sensors were built to target sequences likely to be accessible for binding (Green et al., 2014), and, when tested, yielded fluorescent induction in the presence of GFP (60-fold) and mCherry (13-fold) mRNAs, respectively ( FIGS. 19B-19C ).
  • FIG. 19A As a demonstration of the potential for paper-based synthetic gene networks as an in vitro diagnostics platform, colorimetric mRNA sensors for antibiotic resistance genes were next developed ( FIG. 19A ).
  • mRNA sensors for spectinomycin (5-fold), chloramphenicol (7.5-fold), kanamycin (24-fold) and ampicillin (30-fold) resistance genes yielded significant LacZ induction in the presence of their respective mRNAs (3000 nM, FIGS. 19D and 34 ).
  • the ampicillin resistance mRNA sensor was then tested in the electronic optical reader and found significant detection of target transcripts as low as 3 nM ( FIGS. 19E and 35 ).
  • the signal from the purpose-built device was about three times greater than the plate reader at equivalent trigger RNA concentrations ( FIGS. 19D-19E, 34D ). Tracking the fold change read out over time, it can be seen how the concentration-dependent reaction rate impacts the appearance and duration of the positive signal ( FIG. 35B ).
  • the DNA construct for the nanosensor was freeze-dried along with Hela cell extracts onto paper and the paper discs were rehydrated in the presence or absence of glucose. Upon rehydration, the glucose-related shift was observed, within a physiologically relevant glucose concentration range (0, 5, 10 mM; FIGS. 19H, 36 ). Importantly, in this context, de novo translation of the nanosensor seems to be critical to function; freeze dried preparations of pre-translated protein did not exhibit the characteristic shift in fluorescence.
  • mRNA sensors for the viral pathogen Ebola were built. The goal was to construct and test 24 sensors that could distinguish between the Sudan and Zaire strains of the virus in under a day. Using algorithm, sensors were designed to target mRNA from 12 regions (A-L) of the ORF for the Ebola nucleoprotein gene, which differs in length by only three nucleotides between the Sudan and Zaire strains ( FIG. 39A ).
  • the colorimetric dynamics of the 240 reactions were captured using a plate reader and could be tracked by eye ( FIGS. 39B-39C ).
  • Each of the 24 sensors was triggered in the presence of their target (3000 nM), with maximum induction during the first 90 minutes ranging between 4 to 77 fold. Remarkably, this phase of the screen was completed in less than 12 hours.
  • Four matching sets (D, E, G, H) of the Sudan and Zaire sensors were then selected to test specificity and found a high degree of strain-specific discrimination ( FIG. 39D ), as well as sensitivity down to a concentration of 30 nM trigger RNA for both strains ( FIG. 39E ).
  • T3 RNAP In the presence of DNA encoding the toehold switch and trigger for the T3 module, T3 RNAP is transcribed and translated, which activates T3-mediated transcription and translation of GFP from an otherwise passive component ( FIG. 40B ).
  • T7 RNAP is transcribed, translated and similarly leads to the expression of GFP from a T7-mediated construct ( FIG. 40C ).
  • E. coli RNAP If both the T3 and T7 toehold switch modules are combined, E. coli RNAP generates both T3 and T7 RNAPs. This converging transcription activity leads to their respective trigger and toehold switch RNAs, producing a third route to GFP expression ( FIG. 40D ).
  • This work shows that the platform can sustain multiple rounds of transcription and translation, and be utilized to construct, test and debug complex circuits in a modular fashion.
  • TetR-based GFP and mCherry expression circuits were constructed by inserting GFP or mCherry downstream of the TetR-repressed pLtetO promoter in pZE11 (Lutz and Bujard 1997).
  • tetR was cloned downstream of the constitutive PlacIQ promoter, and this expression cassette was inserted into pZE11-gfp and pZE11-mcherry using XhoI and AatII.
  • FIGS. 37A-37B An overall improvement in fluorescent output from treated paper was found, with 5% BSA yielding the greatest increase ( FIGS. 37A-37B ).
  • FIGS. 37C-37D An overall improvement in fluorescent output from treated paper was found, with 5% BSA yielding the greatest increase.
  • Cell-free reactions were generally assembled (4° C.) as described in the instructions of the respective manufacturers. Briefly, for S30 and S30T7 reactions (Promega, L1020 and L1110), cell extracts and premix containing amino acids were combined at a ratio of 0.33 and 0.51, respectively. The volume was then brought up with RNase inhibitor (Roche; 0.005), plasmid DNA constructs comprising the gene circuits and nuclease-free ddH 2 O. For TetO-based gene circuits, reactions were supplemented with pre-run cell-free reactions expressing constitutive tetR (0.05) to reduce promoter leakage.
  • RNase inhibitor Roche; 0.005
  • TetO-based gene circuits reactions were supplemented with pre-run cell-free reactions expressing constitutive tetR (0.05) to reduce promoter leakage.
  • FIGS. 16B & 16C T7_GFP plasmid DNA 5 ng/ ⁇ l (pBR939b_T7_GFP, Anderson, 2007);
  • FIG. 16E PN25-GFP plasmid DNA 30 ng/ ⁇ l and T7_GFP plasmid DNA 30 ng/ ⁇ l;
  • FIG. 1G Tet-O GFP and TetO-mCherry plasmid DNA 30 ng/ ⁇ l;
  • FIG. 17 linear DNA 33 nM, RNA triggers at 5 ⁇ M;
  • FIG. 18 linear DNA 33 nM, RNA triggers at 5 ⁇ M or as specified;
  • FIGS. 16D & 16E antibiotic resistance gene mRNA sensors for spectinomycin, chloramphenicol, kanamycin and ampicillin linear DNA 33 nM, respective mRNAs at 3 ⁇ M or as specified;
  • FIG. 19F pT7CFE1_GFP plasmid DNA (Thermo Scientific) 30 ng/ ⁇ l, pcDNA3.1 FLIPglu-30uDelta13V plasmid DNA (Takanaga 2010, addgene:18015) 30 ng/ ⁇ l;
  • FIG. 40 T3 and T7 cascade modules plasmid DNA 30 ng/ ⁇ l ( E. coli RNAP_trigger_1, E. coli RNAP_switch_1_T3RNAP, E. coli RNAP_trigger 2, E.
  • RNAP_switch_2_T7RNAP T3_GFP and T7_GFP plasmid DNA 40 ng/ ⁇ l
  • Assembled cell-free reactions were applied (1.8 ⁇ l/disc) to 2 mm paper discs (Whatman, 1442-042), which were then flash frozen in liquid nitrogen and freeze-dried overnight. Paper discs were cut using a 2 mm biopsy punch. Similarly quartz microfiber (Spectrum, 884-66171) was cut and treated with cell-free reactions (3 ⁇ l/disc) prior to freeze-drying. Freeze-dried solution phase reactions (7 ul) were similarly flash frozen and place on the lyophilizer. After 24 hours, reactions were rehydrated with either nuclease-free ddH 2 O or inducer (activated switches) at the concentrations specified. Cell-free reactions without synthetic gene networks were also included to provide the background signal for subtraction from control and treatment reactions.
  • Rehydrated reactions were incubated at 37° C. using either a plate reader (BioTek NEO HTS) or the purpose-built electronic optical reader placed inside a tissue culture incubator.
  • a plate reader BioTek NEO HTS
  • the purpose-built electronic optical reader placed inside a tissue culture incubator.
  • paper discs were placed into black, clear bottom 384 well plates and for the purpose-built reader, paper discs were placed into 2 mm holes cut into the removal acrylic chip ( FIGS. 18H, 38B ).
  • Images of paper discs were collected on a Zeiss Axio Zoom V16 Macroscope (magnification 7 ⁇ ) with an AxioCam MRm in a humidified glass chamber or through the bottom of a clear bottom 384-well plate. Collected images were then stitched together using Zeiss Zen software into large composite images for further processing in ImageJ. Experiments were arranged so that images of control and treatment paper-based reactions were collected together such that parameters could be adjusted for all samples simultaneously. Once optimized, images of individual paper discs were cropped and arrayed into figures. For GFP expression in S30 cell-free system, which exhibits a high level of autofluorescence, a Nuance camera was used to collect multispectral images at between 500 and 620 nM.
  • Perkin Elmer Nuance 3.0.2 software was then used to unmix the spectral signature of the GFP from that of the cell extract.
  • a similar approach was used to create a 410 nm absorbance signature (420 to 720 nM) for image paper discs with p-nitrophenol, the chitinase cleavage product of 4-Nitrophenyl N,N′-diacetyl-beta-D-chitobioside. Images collected with the Nuance camera were scaled using bilinear transformation. For a few composite images, areas around the paper discs were masked to remove extraneous light.
  • Patterns for printed arrays were generated using Adobe Illustrator and then printed onto chromatography paper (Whatman, 3001-861) using a Xerox 8570 printer (Carrilho et al., Anal Chem. 2009, 81(16):7091-5). Once printed, the wax was reflowed using a hot plate (120° C.) so that the wax was present through entire thickness of the paper, creating hydrophobic barriers to contain each reaction.
  • the portable device consists of four layers housed within a laser-cut acrylic box ( FIG. 18H ).
  • the top layer holds 12 LEDs (Digi-Key, 365-1190-ND), which have a very narrow viewing angle and an emission of 570 nM to match the absorbance maximum of the product of the LacZ reaction.
  • the LEDs were placed in close proximity to the chip in the middle layer, which holds 12 paper discs within 2 mm apertures. The apertures prevented transmission of stray light and were coaxial with the LEDs in the top layer, and the array of 12 TSL2561 sensors (Adafruit, 439) in the third layer below.
  • the bottom layer contains the chicken Micro and associated electronics such as the multiplexers (Sparkfun, BOB-09056), breadboard, resistors and connectors. To prevent cross talk between reads, reactions were read in series by sequentially activating each LED and sensor pair. The read frequency and pattern of the reader can be easily adjusted by modifying and uploading alternative sketches to the Engineering Micro. Both the raw data and the data processed using the per disc formula: 100-(100*(Current/Max)), were calculated for each time point and sent to a laptop. A diagram of the circuit and an overview of the laser cut parts can be found in the supplemental figures ( FIGS. 38A-38B ).
  • Fluorescence or absorbance data from the plate reader were first smoothed to reduce measurement noise using a moving three-point average of the time point and the data both preceding and following that read. Background signal was subtracted from each well using the average of control blank reactions that contained the relevant cell-free system alone. The minimum value of each well was then adjusted to zero. For fluorescence data, fold change calculations were done by dividing the wells at each time point by the average signal from the corresponding uninduced control wells. For absorbance measurements, fold change values reflect the difference in the rate of color change between induced and uninduced wells.
  • the Tau test was performed by calculating the difference (Delta) between a measured value (replicate) and the mean of the group. Using the Modified Thompson Tau value for quadruplicate data (1.4250), the test was performed by multiplying the standard deviation of the group by this Tau value. If the resulting number was smaller than the Delta calculated for a measured value, that replicate was considered an outlier and not included in the analysis.
  • the paper-based cell extracts also offer a unique opportunity for molecular biologists to work with difficult-to-culture organisms. By generating cell extracts from engineered cell lines, pathogens or other specialized organisms (i.e., extremophiles, symbionts), these reactions could serve as a proxy for biology that is otherwise inaccessible to the broad research community.
  • the incorporation of human cell extracts into the paper-based scheme is an exciting feature that leads to the prospect of diagnostic and synthetic biology applications based on the thousands of human and mammalian transcription factors (Hughes, 2011), such as nuclear receptors, with complex and nuanced regulatory features, including small molecule-responsive regulation (Pardee et al., 2009).
  • toehold switch mRNA sensors offer a sequence-based method of detection that means research and clinical tools can be designed rationally, lowering development costs and allowing for significantly shorter design-to-production cycles.
  • novel mRNA sensors were presented, including 24 Ebola sensors constructed in less than 12 hours.
  • the DNA input cost for the Ebola series was $21 USD/sensor.
  • Paper-based synthetic gene networks are also potentially less expensive to manufacture than most of the standard of care options currently available. At the moment, the cost of a 1 ⁇ l paper-based sensor would be between 35 ⁇ -65 ⁇ using commercial cell-free expression systems. However, these systems can be readily produced in house, reducing the cost to as little as 2 ⁇ -4 ⁇ per sensor (http://www.openwetware.org/wiki/Biomolecular_Breadboards:Protocols:cost_estimate). This compares to $0.45-$1.40 for a single RDT reaction and $1.50-$4.00 (reagents only) for PCR (Cordary, Am. J. Trop. Med. Hyg., 2012, 87, 223-230).
  • Transcription- and translation-based detection is also competitive with regards to time to detection.
  • detection of mRNA from the ampicillin resistance gene was recorded as early as 20 minutes for high concentrations of mRNA and about 40 minutes for the 3 nM treatment ( FIGS. 19E, 35 ).
  • This compares favorably to RDTs, which can detect a single antigen in ⁇ 20 minutes, or PCR, which can take 1.5 to 2 hours and is largely confined to laboratory settings (Cordary, Am. J. Trop. Med. Hyg., 2012, 87, 223-230).
  • Paper-based synthetic gene networks can significantly expand the role of synthetic biology in the clinic, global health, industry, research and education.

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